z_offSet = -20
) %>%
setSpin()
-
-In the view above, we see the blue peptide and the red HLA-B protein.
+
+In the view above, we see the blue peptide and the red HLA-B protein.
The tyrosine at position 9 is highlighted with a ball+stick
representation, and it is also labeled with a text label. The structure
is rotating so we can getter a better view.
diff --git a/pkgdown.yml b/pkgdown.yml
index 50f9856..27dd21e 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -4,7 +4,7 @@ pkgdown_sha: ~
articles:
examples: examples.html
visualize-hla-structure: visualize-hla-structure.html
-last_built: 2023-11-27T23:51Z
+last_built: 2023-11-29T16:25Z
urls:
reference: https://slowkow.github.io/hlabud/reference
article: https://slowkow.github.io/hlabud/articles
diff --git a/search.json b/search.json
index 6081911..150d748 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://slowkow.github.io/hlabud/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://slowkow.github.io/hlabud/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"hlabud usage examples","text":"Kamil Slowikowski 2023-11-27 hlabud R package provides functions facilitate download analysis human leukocyte antigen (HLA) genotype sequence alignments IMGTHLA R. Let’s consider question might want answer HLA genotypes. amino acid positions different DRB1*04:174 DRB1*15:152 genotypes? hlabud, can find answer lines code: two genotypes nearly identical, amino acid position 9 different: position 9 E (Glu) DRB1*04:174 position 9 W (Trp) DRB1*15:152 just easy find nucleotides distinguish two alleles:","code":"library(hlabud) a <- hla_alignments(\"DRB1\") dosage(c(\"DRB1*04:174\", \"DRB1*15:152\"), a$onehot) #> pos9_E pos9_W #> DRB1*04:174 1 0 #> DRB1*15:152 0 1 n <- hla_alignments(\"DRB1\", type = \"nuc\") dosage(c(\"DRB1*04:174\", \"DRB1*15:152\"), n$onehot) #> pos109_C pos109_T #> DRB1*04:174 0 1 #> DRB1*15:152 1 0"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"hlabud usage examples","text":"quickest way get hlabud install GitHub: , included usage examples. hope inspire share HLA analyses. source code page available . Thank reporting issues hlabud.","code":"# install.packages(\"devtools\") devtools::install_github(\"slowkow/hlabud\")"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"get-a-one-hot-encoded-matrix-for-all-hla-drb1-alleles","dir":"Articles","previous_headings":"","what":"Get a one-hot encoded matrix for all HLA-DRB1 alleles","title":"hlabud usage examples","text":"can use hla_alignments(\"DRB1\") load DRB1_prot.txt file latest IMGTHLA release: object list three items: $sequences amino acid sequence alignments data frame: conventions used alignments (copied EBI): entry allele displayed respect reference sequences. identity reference sequence present base displayed hyphen (-). Non-identity reference sequence shown displaying appropriate base position. insertion deletion occurred represented period (.). sequence unknown point alignment, represented asterisk (*). protein alignments null alleles, ‘Stop’ codons represented hash (X). protein alignments, sequence following termination codon, marked appear blank. conventions used nucleotide protein alignments. Learn alignments : https://www.ebi.ac.uk/ipd/imgt/hla/alignment/help/ $alleles matrix amino acids one column position: $onehot one-hot encoded matrix one column amino acid position:","code":"library(hlabud) a <- hla_alignments(gene = \"DRB1\", verbose = TRUE) #> Reading /home/runner/.local/share/hlabud/.354.0/alignments/DRB1_prot.txt str(a) #> List of 3 #> $ sequences: tibble [3,588 × 2] (S3: tbl_df/tbl/data.frame) #> ..$ allele: chr [1:3588] \"DRB1*01:01:01:01\" \"DRB1*01:01:01:02\" \"DRB1*01:01:01:03\" \"DRB1*01:01:01:04\" ... #> ..$ seq : chr [1:3588] \"MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVR.LLERCIYNQEE.SVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCR\"| __truncated__ \"------------------------------------------------------.-----------.--------------------------------------------\"| __truncated__ \"------------------------------------------------------.-----------.--------------------------------------------\"| __truncated__ \"------------------------------------------------------.-----------.--------------------------------------------\"| __truncated__ ... #> $ alleles : chr [1:3588, 1:288] \"M\" \"M\" \"M\" \"M\" ... #> ..- attr(*, \"dimnames\")=List of 2 #> .. ..$ : chr [1:3588] \"DRB1*01:01:01:01\" \"DRB1*01:01:01:02\" \"DRB1*01:01:01:03\" \"DRB1*01:01:01:04\" ... #> .. ..$ : chr [1:288] \"posn29\" \"posn28\" \"posn27\" \"posn26\" ... #> $ onehot : num [1:3588, 1:1786] 0 0 0 0 0 0 0 0 0 0 ... #> ..- attr(*, \"dimnames\")=List of 2 #> .. ..$ : chr [1:3588] \"DRB1*01:01:01:01\" \"DRB1*01:01:01:02\" \"DRB1*01:01:01:03\" \"DRB1*01:01:01:04\" ... #> .. ..$ : chr [1:1786] \"posn29_unk\" \"posn29_M\" \"posn28_unk\" \"posn28_L\" ... a$sequences #> # A tibble: 3,588 × 2 #> allele seq #> #> 1 DRB1*01:01:01:01 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVR.LLER… #> 2 DRB1*01:01:01:02 ------------------------------------------------------.----… #> 3 DRB1*01:01:01:03 ------------------------------------------------------.----… #> 4 DRB1*01:01:01:04 ------------------------------------------------------.----… #> 5 DRB1*01:01:01:05 ------------------------------------------------------.----… #> 6 DRB1*01:01:01:06 ------------------------------------------------------.----… #> 7 DRB1*01:01:01:07 ------------------------------------------------------.----… #> 8 DRB1*01:01:01:08 ------------------------------------------------------.----… #> 9 DRB1*01:01:01:09 ------------------------------------------------------.----… #> 10 DRB1*01:01:01:10 ------------------------------------------------------.----… #> # ℹ 3,578 more rows a$alleles[1:5,1:7] #> posn29 posn28 posn27 posn26 posn25 posn24 posn23 #> DRB1*01:01:01:01 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" \"P\" #> DRB1*01:01:01:02 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" \"P\" #> DRB1*01:01:01:03 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" \"P\" #> DRB1*01:01:01:04 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" \"P\" #> DRB1*01:01:01:05 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" \"P\" a$onehot[1:5,1:7] #> posn29_unk posn29_M posn28_unk posn28_L posn28_V posn27_unk #> DRB1*01:01:01:01 0 1 0 0 1 0 #> DRB1*01:01:01:02 0 1 0 0 1 0 #> DRB1*01:01:01:03 0 1 0 0 1 0 #> DRB1*01:01:01:04 0 1 0 0 1 0 #> DRB1*01:01:01:05 0 1 0 0 1 0 #> posn27_C #> DRB1*01:01:01:01 1 #> DRB1*01:01:01:02 1 #> DRB1*01:01:01:03 1 #> DRB1*01:01:01:04 1 #> DRB1*01:01:01:05 1"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"convert-genotypes-to-a-dosage-matrix","dir":"Articles","previous_headings":"","what":"Convert genotypes to a dosage matrix","title":"hlabud usage examples","text":"Suppose individuals following genotypes: want run association test amino acid positions, need convert genotype names matrix allele dosages (e.g., 0, 1, 2). can use dosage() convert individual’s genotypes amino acid dosages: Note: dosage matrix one row individual one column amino acid position. default, dosage() discard columns individuals identical. first individual dosage=3 pos6_R (position 6 Arg). ’s assigned individual 3 alleles input. Please careful check data looks way expect!","code":"genotypes <- c( \"DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02\", \"DRB1*04:174,DRB1*15:152\", \"DRB1*04:56:02,DRB1*15:01:48\", \"DRB1*14:172,DRB1*04:160\", \"DRB1*04:359,DRB1*04:284:02\" ) dosage <- dosage(genotypes, a$onehot) dosage[,1:4] #> posn29_unk posn29_M pos6_R #> DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02 1 2 3 #> DRB1*04:174,DRB1*15:152 2 0 2 #> DRB1*04:56:02,DRB1*15:01:48 2 0 2 #> DRB1*14:172,DRB1*04:160 2 0 2 #> DRB1*04:359,DRB1*04:284:02 2 0 2 #> pos9_E #> DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02 3 #> DRB1*04:174,DRB1*15:152 1 #> DRB1*04:56:02,DRB1*15:01:48 1 #> DRB1*14:172,DRB1*04:160 2 #> DRB1*04:359,DRB1*04:284:02 2 dim(dosage) #> [1] 5 38"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"logistic-regression-association-for-amino-acid-positions","dir":"Articles","previous_headings":"","what":"Logistic regression association for amino acid positions","title":"hlabud usage examples","text":"Let’s simulate dataset cases controls demonstrate one approach testing amino acid positions might associated cases. simulated dataset 100 individuals, 52 cases 48 controls. also one column amino acid position might want test association case variable. One possible approach association testing use glm() fit logistic regression model amino acid position. reveal amino acid position might associated case variable simulated dataset. volcano shows Odds Ratio P-value amino acid position. top hits P < 0.05 labeled. simulation, case variable associated pos123_S (P = 0.026, = 0.52, 95% CI 0.28 0.91).","code":"set.seed(2) n <- 100 d <- data.frame( geno = paste( sample(rownames(a$onehot), n, replace = TRUE), sample(rownames(a$onehot), n, replace = TRUE), sep = \",\" ), age = sample(21:100, n, replace = TRUE), case = sample(0:1, n, replace = TRUE) ) d <- cbind(d, dosage(d$geno, a$onehot)) d[1:5,1:6] #> geno age case #> DRB1*04:256,DRB1*04:125 DRB1*04:256,DRB1*04:125 55 0 #> DRB1*04:11:01:02,DRB1*01:02:12 DRB1*04:11:01:02,DRB1*01:02:12 73 1 #> DRB1*14:08,DRB1*15:01:02 DRB1*14:08,DRB1*15:01:02 72 0 #> DRB1*03:90,DRB1*04:278 DRB1*03:90,DRB1*04:278 22 1 #> DRB1*03:67N,DRB1*03:100:02 DRB1*03:67N,DRB1*03:100:02 34 0 #> posn29_unk posn29_M posn25_K #> DRB1*04:256,DRB1*04:125 2 0 0 #> DRB1*04:11:01:02,DRB1*01:02:12 1 1 1 #> DRB1*14:08,DRB1*15:01:02 0 2 1 #> DRB1*03:90,DRB1*04:278 2 0 0 #> DRB1*03:67N,DRB1*03:100:02 2 0 0 # select the amino acid positions that have at least 3 people with dosage > 0 my_as <- names(which(colSums(d[,4:ncol(d)] > 0) >= 3)) # run the association tests my_glm <- rbindlist(pblapply(my_as, function(my_a) { f <- sprintf(\"case ~ %s\", my_a) glm(as.formula(f), data = d, family = \"binomial\") %>% parameters(exponentiate = TRUE) })) # look at the top hits my_glm %>% arrange(p) %>% filter(!Parameter %in% c(\"(Intercept)\")) %>% head #> Parameter Coefficient SE CI CI_low CI_high z #> 1: pos123_S 0.5161604 0.1528830 0.95 0.282671869 0.9100318 -2.232794 #> 2: pos183_V 0.5570074 0.1572414 0.95 0.314570198 0.9582010 -2.072913 #> 3: pos34_H 2.1982280 0.8658531 0.95 1.053839944 5.0273874 1.999690 #> 4: pos51_A 0.1170213 0.1265210 0.95 0.006179376 0.6749415 -1.984314 #> 5: pos107_S 0.5815232 0.1638237 0.95 0.329174623 1.0003310 -1.924302 #> 6: pos69_L 1.6740699 0.4630002 0.95 0.982434872 2.9247856 1.863017 #> df_error p #> 1: Inf 0.02556252 #> 2: Inf 0.03818041 #> 3: Inf 0.04553374 #> 4: Inf 0.04722090 #> 5: Inf 0.05431680 #> 6: Inf 0.06245981"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"umap-embedding-of-3588-hla-drb1-alleles","dir":"Articles","previous_headings":"","what":"UMAP embedding of 3,588 HLA-DRB1 alleles","title":"hlabud usage examples","text":"many possibilities analysis one-hot encoding HLA-DRB1 alleles. example, UMAP embedding 3,588 HLA-DRB1 alleles encoded one-hot amino acid matrix 1786 columns, one amino acid position. can highlight alleles amino acid H position 13: can represent amino acid position 13 different color:","code":"uamp(a$onehot, n_epochs = 200, min_dist = 1, spread = 2)"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"get-hla-allele-frequencies-from-allele-frequency-net-database-afnd","dir":"Articles","previous_headings":"","what":"Get HLA allele frequencies from Allele Frequency Net Database (AFND)","title":"hlabud usage examples","text":"Download read table HLA allele frequencies Allele Frequency Net Database (AFND). use data, please cite latest manuscript Allele Frequency Net Database: Gonzalez-Galarza FF, McCabe , Santos EJMD, Jones J, Takeshita L, Ortega-Rivera ND, et al. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data new query tools. Nucleic Acids Res. 2020;48: D783–D788. doi:10.1093/nar/gkz1029 Plot frequency specific allele (DQB1*02:01) populations 1000 sampled individuals: See github.com/slowkow/allelefrequencies examples might use data.","code":"af <- hla_frequencies() af #> # A tibble: 123,502 × 7 #> group gene allele population indivs_over_n alleles_over_2n n #> #> 1 hla A A*01:01 Argentina Rosario To… 15.1 0.076 86 #> 2 hla A A*01:01 Armenia combined Reg… NA 0.125 100 #> 3 hla A A*01:01 Australia Cape York … NA 0.053 103 #> 4 hla A A*01:01 Australia Groote Eyl… NA 0.027 75 #> 5 hla A A*01:01 Australia New South … NA 0.187 134 #> 6 hla A A*01:01 Australia Yuendumu A… NA 0.008 191 #> 7 hla A A*01:01 Austria 27 0.146 200 #> 8 hla A A*01:01 Azores Central Islan… NA 0.08 59 #> 9 hla A A*01:01 Azores Oriental Isla… NA 0.115 43 #> 10 hla A A*01:01 Azores Terceira Isla… NA 0.109 130 #> # ℹ 123,492 more rows my_allele <- \"DQB1*02:01\" my_af <- af %>% filter(allele == my_allele) %>% filter(n > 1000) %>% arrange(-alleles_over_2n) ggplot(my_af) + aes(x = alleles_over_2n, y = reorder(population, alleles_over_2n)) + scale_y_discrete(position = \"right\") + geom_colh() + labs( x = \"Allele Frequency (Alleles / 2N)\", y = NULL, title = glue(\"Frequency of {my_allele} across {length(unique(my_af$population))} populations\"), caption = \"Data from AFND http://allelefrequencies.net\" )"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"compute-hla-divergence-with-the-grantham-distance-matrix","dir":"Articles","previous_headings":"","what":"Compute HLA divergence with the Grantham distance matrix","title":"hlabud usage examples","text":"HLA allele binds specific set peptides. , individual two highly dissimilar alleles can bind greater number different peptides homozygous individual (https://doi.org/10.1007/BF02918202): MHC class II allele capacity bind present specific set peptides processed antigens. inability specific class II allele bind present fragment derived processed antigen results loss immune responsiveness antigen individuals homozygous class II allele. can compute HLA divergence metric set individuals like : divergence homozygote equal zero, definition: default, use amino acid distance matrix Granthan 1974 (https://doi.org/10.1126/science.185.4154.862). Alternatively, can choose use uniform matrix instead (diagonal values 0, non-diagonal values equal 1): amino acid distance matrix easily accessible, provide two built-options \"grantham\" \"uniform\":","code":"my_genos <- c(\"A*23:01:12,A*24:550\", \"A*25:12N,A*11:27\", \"A*24:381,A*33:85\") hla_divergence(my_genos, method = \"grantham\") #> A*23:01:12,A*24:550 A*25:12N,A*11:27 A*24:381,A*33:85 #> 0.4924242 3.3333333 4.9015152 hla_divergence(\"A*01:01,A*01:01\") #> A*01:01,A*01:01 #> 0 hla_divergence(my_genos, method = \"uniform\") #> A*23:01:12,A*24:550 A*25:12N,A*11:27 A*24:381,A*33:85 #> 0.007575758 0.040404040 0.060606061 amino_distance_matrix(method = \"uniform\") #> A R N D C Q E G H I L K M F P S T W Y V #> A 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> R 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> N 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> D 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> C 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> Q 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> E 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 #> G 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 #> H 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 #> I 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 #> L 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 #> K 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 #> M 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 #> F 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 #> P 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 #> S 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 #> T 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 #> W 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 #> Y 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 #> V 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"download-and-unpack-all-data-from-the-latest-imgthla-release","dir":"Articles","previous_headings":"","what":"Download and unpack all data from the latest IMGTHLA release","title":"hlabud usage examples","text":"want use hla_alignments(), don’t need install_hla() data files downloaded automatically needed cached future use. users might need access additional files present full data release. Run install_hla() download unpack latest IMGTHLA release. destination folder downloaded data files getOption(\"hlabud_dir\") (automatically tailored operating system thanks rappdirs package). examples download releases get list release names. Download latest release (default) specific release: Optionally, get set directory hlabud uses store data: List releases: installing releases, hlabud folder might look like :","code":"# Download all of the data (120MB) for the latest IMGTHLA release install_hla(release = \"latest\") # Download a specific release install_hla(release = \"3.51.0\") getOption(\"hlabud_dir\") #> [1] \"/home/username/.local/share/hlabud\" # Manually override the directory for hlabud to use options(hlabud_dir = \"/path/to/my/dir\") hla_releases() #> [1] \"3.51.0\" \"3.50.0\" \"3.49.0\" \"3.48.0\" \"3.47.0\" \"3.46.0\" \"3.45.1\" \"3.45.01\" #> [9] \"3.45.0.1\" \"3.45.0\" \"3.44.1\" \"3.44.0\" \"3.43.0\" \"3.42.0\" \"3.41.2\" \"3.41.0\" #> [17] \"3.40.0\" \"3.39.0\" \"3.38.0\" \"3.37.0\" \"3.36.0\" \"3.35.0\" \"3.34.0\" \"3.33.0\" #> [25] \"3.32.0\" \"3.31.0\" \"3.30.0\" \"3.29.0\" \"3.28.0\" \"3.27.0\" ❯ ls -lah \"/home/user/.local/share/hlabud\" total 207M drwxrwxr-x 3 user user 32 Apr 5 01:19 3.30.0 drwxrwxr-x 11 user user 4.0K Apr 7 19:31 3.40.0 drwxrwxr-x 12 user user 4.0K Apr 5 00:27 3.51.0 -rw-rw-r-- 1 user user 15K Apr 7 19:23 tags.json -rw-rw-r-- 1 user user 79M Apr 7 19:28 v3.40.0-alpha.tar.gz -rw-rw-r-- 1 user user 129M Apr 4 20:07 v3.51.0-alpha.tar.gz"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"count-the-number-of-alleles-in-each-imgthla-release","dir":"Articles","previous_headings":"","what":"Count the number of alleles in each IMGTHLA release","title":"hlabud usage examples","text":"can get list release names: can get allele names release: Next, count many alleles release: plot number alleles line plot:","code":"releases <- hla_releases() releases #> [1] \".354.0\" \"3.53.0\" \"3.52.0\" \"3.51.0\" \"3.50.0\" \"3.49.0\" #> [7] \"3.48.0\" \"3.47.0\" \"3.46.0\" \"3.45.1\" \"3.45.01\" \"3.45.0.1\" #> [13] \"3.45.0\" \"3.44.1\" \"3.44.0\" \"3.43.0\" \"3.42.0\" \"3.41.2\" #> [19] \"3.41.0\" \"3.40.0\" \"3.39.0\" \"3.38.0\" \"3.37.0\" \"3.36.0\" #> [25] \"3.35.0\" \"3.34.0\" \"3.33.0\" \"3.32.0\" \"3.31.0\" \"3.30.0\" my_alleles <- rbindlist(lapply(releases, function(release) { retval <- hla_alleles(release = release) retval$release <- release return(retval) }), fill = TRUE) #> Warning in hla_alleles(release = release): unrecognized release name #> 'Allelelist.3451.txt' #> Warning in hla_alleles(release = release): unrecognized release name #> 'Allelelist.34501.txt' #> Warning in hla_alleles(release = release): unrecognized release name #> 'Allelelist.34501.txt' #> Warning in hla_alleles(release = release): unrecognized release name #> 'Allelelist.3441.txt' #> Warning in hla_alleles(release = release): unrecognized release name #> 'Allelelist.3412.txt' d <- my_alleles %>% count(release) %>% filter(n > 1) d #> release n #> 1: .354.0 38416 #> 2: 3.30.0 17509 #> 3: 3.31.0 17874 #> 4: 3.32.0 18363 #> 5: 3.33.0 18955 #> 6: 3.34.0 20272 #> 7: 3.35.0 21683 #> 8: 3.36.0 22548 #> 9: 3.37.0 24093 #> 10: 3.38.0 25958 #> 11: 3.39.0 26512 #> 12: 3.40.0 27273 #> 13: 3.41.0 27980 #> 14: 3.42.0 28786 #> 15: 3.43.0 29417 #> 16: 3.44.0 30523 #> 17: 3.45.0 31552 #> 18: 3.46.0 32330 #> 19: 3.47.0 33552 #> 20: 3.48.0 34145 #> 21: 3.49.0 35077 #> 22: 3.50.0 36016 #> 23: 3.51.0 36625 #> 24: 3.52.0 37068 #> 25: 3.53.0 37619 #> release n ggplot(d) + aes(x = release, y = n, group = 1) + geom_line() + geom_text(aes(label = release), hjust = 1) + labs(x = NULL, y = \"Number of alleles\", title = \"Each release has more HLA alleles\") + theme( axis.text.x = element_blank(), axis.ticks.x = element_blank(), ) d2 <- my_alleles %>% mutate(gene = str_split_fixed(Allele, \"\\\\*\", 2)[,1]) %>% count(release, gene) ggplot() + aes(x = release, y = n) + geom_line( data = d2, aes(group = gene, color = gene) ) + scale_color_discrete(guide = \"none\") + geom_text( data = d2 %>% filter(release == \"3.52.0\"), mapping = aes(label = gene), hjust = 0 ) + labs(x = NULL, y = \"Number of alleles\", title = \"Number of alleles per release and gene\") + scale_x_discrete(expand = expansion(mult = c(0.01, 0.1))) + scale_y_log10() + theme( panel.grid.major.y = element_line(), axis.text.x = element_blank(), axis.ticks.x = element_blank(), )"},{"path":"https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Visualize HLA protein structures","text":"Kamil Slowikowski 2023-11-27 vignette, explore different methods visualizing molecular structure HLA proteins. First, ’ll look example use NGLVieweR R package show HLA protein structures. Next, ’ll use PyMOL thing.","code":""},{"path":"https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html","id":"what-are-the-pdb-identifiers-for-each-hla-gene","dir":"Articles","previous_headings":"","what":"What are the PDB identifiers for each HLA gene?","title":"Visualize HLA protein structures","text":"list PDB identifiers might consider using represent HLA protein: Also try searching PDB website , e.g., \"HLA-DR\" see appropriate structure analysis.","code":"HLA-A 2xpg HLA-B 2bvp HLA-C 4nt6 HLA-DP 3lqz HLA-DQ 4z7w HLA-DR 3pdo"},{"path":"https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html","id":"using-nglviewer","dir":"Articles","previous_headings":"","what":"Using NGLVieweR","title":"Visualize HLA protein structures","text":"Let’s try visualize position 9 HLA-B protein structure. visualize structure 2bvp Protein Data Bank (PDB). example NGLVieweR R package Niels van der Velden: view , see blue peptide red HLA-B protein. tyrosine position 9 highlighted ball+stick representation, also labeled text label. structure rotating can getter better view. can use hlabud answer questions HLA-B Tyr9 (tyrosine position 9). example, HLA-B alleles amino acid position? fraction reported HLA-B alleles Tyr9?","code":"# devtools::install_github(\"nvelden/NGLVieweR\") # we need the latest version library(NGLVieweR) library(magrittr) my_sele <- \"9:A\" NGLVieweR(\"2bvp\") %>% stageParameters( backgroundColor = \"white\", zoomSpeed = 1, cameraFov = 80 ) %>% addRepresentation( type = \"cartoon\" ) %>% addRepresentation( type = \"ball+stick\", param = list( sele = my_sele ) ) %>% addRepresentation( type = \"label\", param = list( sele = my_sele, labelType = \"format\", labelFormat = \"[%(resname)s]%(resno)s\", # or enter custom text labelGrouping = \"residue\", # or \"atom\" (eg. sele = \"20:A.CB\") color = \"black\", fontFamiliy = \"sans-serif\", xOffset = 1, yOffset = 0, zOffset = 0, fixedSize = TRUE, radiusType = 1, radiusSize = 5.5, # Label size showBackground = TRUE # backgroundColor=\"black\", # backgroundOpacity=0.5 ) ) %>% zoomMove( center = my_sele, zoom = my_sele, duration = 0, # animation time in ms z_offSet = -20 ) %>% setSpin() library(hlabud) a <- hla_alignments(\"B\") head(names(which(a$onehot[,\"pos9_Y\"] == 1))) #> [1] \"B*07:02:01:01\" \"B*07:02:01:02\" \"B*07:02:01:03\" \"B*07:02:01:04\" #> [5] \"B*07:02:01:05\" \"B*07:02:01:06\" sum(a$onehot[,\"pos9_Y\"] == 1) / nrow(a$onehot) #> [1] 0.7101798"},{"path":"https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html","id":"using-pymol","dir":"Articles","previous_headings":"","what":"Using PyMOL","title":"Visualize HLA protein structures","text":"PyMOL one favorite methods visualizing protein structures, allows us change residue existing protein visualize new mutated protein. takes lines PyMOL create nice figure. example, want quickly highlight positions 13 45 HLA-DQB1, snippet PyMOL code produce figure . Bash script : Write PyMOL script Run PyMOL script pymol command PyMOL script : Load structure Protein Data Bank (PDB). 7kei identifier published protein structure. Color HLA-DQA1 protein teal. Color HLA-DQB1 protein orange. Color peptide purple. color residues 13 45 HLA-DQB1 red. Label residues positions names. Write PNG file view structure. image , manually rotated structure mouse added text labels like \"PDB: 7kei\" saving file.","code":"#!/usr/bin/env bash # Write a pymol script cat << EOF > script.pml fetch 7kei show cartoon remove solvent remove chain D remove chain H color teal, chain A color orange, chain B color purple, chain C color red, chain B & resi 13 color red, chain B & resi 45 label n. CA and chain B & resi 13, \"%s %s\" % (resi, resn) label n. CA and chain B & resi 45, \"%s %s\" % (resi, resn) png 7kei.png, width=1200, height=800, dpi=300 EOF # On Linux, we can just use `pymol` without making an alias # On macOS, we need to make an alias alias pymol=/Applications/PyMOL.app/Contents/MacOS/PyMOL pymol -c script.pml"},{"path":"https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html","id":"other-pdb-viewers","dir":"Articles","previous_headings":"","what":"Other PDB viewers","title":"Visualize HLA protein structures","text":"Python: https://github.com/nglviewer/nglview Javascript: https://www.rcsb.org/3d-view https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=7kei&bu=1 https://github.com/nglviewer/ngl https://github.com/biasmv/pv R: https://www.raymolecule.com","code":""},{"path":"https://slowkow.github.io/hlabud/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Kamil Slowikowski. Author, maintainer.","code":""},{"path":"https://slowkow.github.io/hlabud/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"J R, DJ B, X G, MA C, P F, SGE. M (2019). “IPD-IMGT/HLA Database.” Nucleic Acids Research, 48(D1), D948–D955. doi:10.1093/nar/gkz950. Slowikowski K (2023). hlabud: IMGTHLA Data R. doi:10.5281/zenodo.8183949, R package version 1.0.0.9999, https://github.com/slowkow/hlabud.","code":"@Article{, author = {Robinson J and Barker DJ and Georgiou X and Cooper MA and Flicek P and Marsh SGE.}, title = {IPD-IMGT/HLA Database}, doi = {10.1093/nar/gkz950}, year = {2019}, month = {oct}, publisher = {Oxford University Press}, volume = {48}, number = {D1}, pages = {D948–D955}, journal = {Nucleic Acids Research}, } @Manual{, title = {{hlabud}: IMGTHLA Data from R}, author = {Kamil Slowikowski}, year = {2023}, note = {R package version 1.0.0.9999}, doi = {10.5281/zenodo.8183949}, url = {https://github.com/slowkow/hlabud}, }"},{"path":"https://slowkow.github.io/hlabud/index.html","id":"hlabud-hla-analysis-in-r-","dir":"","previous_headings":"","what":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","title":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","text":"hlabud provides methods retrieve sequence alignment data IMGTHLA convert data convenient R matrices ready downstream analysis. See usage examples learn use data logistic regression dimensionality reduction. also share tips visualize 3D molecular structure HLA proteins highlight specific amino acid residues. example, let’s consider simple question two HLA genotypes DRB1*04:174 DRB1*15:152. amino acid positions different two genotypes? output, can conclude two genotypes nearly identical, different amino acids E W position 9.","code":"library(hlabud) a <- hla_alignments(\"DRB1\") dosage(c(\"DRB1*04:174\", \"DRB1*15:152\"), a$onehot) ## pos9_E pos9_W ## DRB1*04:174 1 0 ## DRB1*15:152 0 1"},{"path":"https://slowkow.github.io/hlabud/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","text":"quickest way get hlabud install GitHub:","code":"# install.packages(\"devtools\") devtools::install_github(\"slowkow/hlabud\")"},{"path":"https://slowkow.github.io/hlabud/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","text":"See usage examples get ideas use hlabud analyses. Get one-hot encoded matrix HLA-DRB1 alleles Convert genotypes dosage matrix Logistic regression association amino acid positions UMAP embedding 3,516 HLA-DRB1 alleles Get HLA allele frequencies Allele Frequency Net Database (AFND) Compute HLA divergence Grantham distance matrix Download unpack data latest IMGTHLA release","code":""},{"path":"https://slowkow.github.io/hlabud/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","text":"hlabud provides access data IMGT/HLA database. Therefore, use hlabud please cite IMGT/HLA paper: Robinson J, Barker DJ, Georgiou X, Cooper MA, Flicek P, Marsh SGE. IPD-IMGT/HLA Database. Nucleic Acids Res. 2020;48: D948–D955. doi:10.1093/nar/gkz950 hlabud also provides access data Allele Frequency Net Database (AFND). Therefore, use hlabud::hla_frequencies() please cite AFND paper: Gonzalez-Galarza FF, McCabe , Santos EJMD, Jones J, Takeshita L, Ortega-Rivera ND, et al. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data new query tools. Nucleic Acids Res. 2020;48: D783–D788. doi:10.1093/nar/gkz1029 Additionally, can also cite hlabud package like : Slowikowski K. hlabud: methods access analysis human leukocyte antigen (HLA) gene sequence alignments IMGT/HLA. R package version 1.0.0.","code":""},{"path":"https://slowkow.github.io/hlabud/index.html","id":"related-work","dir":"","previous_headings":"","what":"Related work","title":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","text":"recommend article anyone new HLA, beautiful figures help build intuition: La Gruta NL, Gras S, Daley SR, Thomas PG, Rossjohn J. Understanding drivers MHC restriction T cell receptors. Nat Rev Immunol. 2018;18: 467–478. Learn conventions HLA nomenclature: Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, et al. Nomenclature factors HLA system, 2010. Tissue Antigens. 2010;75: 291–455. case-control analysis HLA genotype data, consider BIGDAWG R package available CRAN. related article: Pappas DJ, Marin W, Hollenbach JA, Mack SJ. Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): integrated case-control analysis pipeline. Hum Immunol. 2016;77: 283–287.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/amino_distance_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","title":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","text":"default, return amino acid distance matrix Grantham 1974 (doi:10.1126/science.185.4154.862).","code":""},{"path":"https://slowkow.github.io/hlabud/reference/amino_distance_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","text":"","code":"amino_distance_matrix(method = \"grantham\")"},{"path":"https://slowkow.github.io/hlabud/reference/amino_distance_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","text":"method \"grantham\" Grantham 1974 matrix \"uniform\" matrix ones non-diagonal.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/amino_distance_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","text":"20x20 symmetric matrix positive numbers zeros diagonal.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/amino_distance_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","text":"","code":"# By default, the Grantham 1974 matrix amino_distance_matrix(\"grantham\") #> A R N D C Q E G H I L K M F P S T W Y #> A 0 112 111 126 195 91 107 60 86 94 96 106 84 113 27 99 58 148 112 #> R 112 0 86 96 180 43 54 125 29 97 102 26 91 97 103 110 71 101 77 #> N 111 86 0 23 139 46 42 80 68 149 153 94 142 158 91 46 65 174 143 #> D 126 96 23 0 154 61 45 94 81 168 172 101 160 177 108 65 85 181 160 #> C 195 180 139 154 0 154 170 159 174 198 198 202 196 205 169 112 149 215 194 #> Q 91 43 46 61 154 0 29 87 24 109 113 53 101 116 76 68 42 130 99 #> E 107 54 42 45 170 29 0 98 40 134 138 56 126 140 93 80 65 152 122 #> G 60 125 80 94 159 87 98 0 98 135 138 127 127 153 42 56 59 184 147 #> H 86 29 68 81 174 24 40 98 0 94 99 32 87 100 77 89 47 115 83 #> I 94 97 149 168 198 109 134 135 94 0 5 102 10 21 95 142 89 61 33 #> L 96 102 153 172 198 113 138 138 99 5 0 107 15 22 98 145 92 61 36 #> K 106 26 94 101 202 53 56 127 32 102 107 0 95 102 103 121 78 110 85 #> M 84 91 142 160 196 101 126 127 87 10 15 95 0 28 87 135 81 67 36 #> F 113 97 158 177 205 116 140 153 100 21 22 102 28 0 114 155 103 40 22 #> P 27 103 91 108 169 76 93 42 77 95 98 103 87 114 0 74 38 147 110 #> S 99 110 46 65 112 68 80 56 89 142 145 121 135 155 74 0 58 177 144 #> T 58 71 65 85 149 42 65 59 47 89 92 78 81 103 38 58 0 128 92 #> W 148 101 174 181 215 130 152 184 115 61 61 110 67 40 147 177 128 0 37 #> Y 112 77 143 160 194 99 122 147 83 33 36 85 36 22 110 144 92 37 0 #> V 64 96 133 152 192 96 121 109 84 29 32 97 21 50 68 124 69 88 55 #> V #> A 64 #> R 96 #> N 133 #> D 152 #> C 192 #> Q 96 #> E 121 #> G 109 #> H 84 #> I 29 #> L 32 #> K 97 #> M 21 #> F 50 #> P 68 #> S 124 #> T 69 #> W 88 #> Y 55 #> V 0 # All ones, and zeros on the diagonal amino_distance_matrix(\"uniform\") #> A R N D C Q E G H I L K M F P S T W Y V #> A 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> R 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> N 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> D 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> C 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> Q 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> E 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 #> G 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 #> H 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 #> I 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 #> L 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 #> K 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 #> M 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 #> F 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 #> P 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 #> S 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 #> T 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 #> W 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 #> Y 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 #> V 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0"},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"genotype name, return dosage matrix residue (amino acid nucleotide) position.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"","code":"dosage(names, mat, drop_constants = TRUE, drop_duplicates = TRUE)"},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"names Input character vector one genotype individual. entries must present rownames(mat). mat one-hot encoded matrix one row per allele one column residue (amino acid nucleotide) position. drop_constants Filter constant amino acid positions default. drop_duplicates Filter duplicate amino acid positions default.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"matrix one row input genotype, one column residue position.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"genotype represented like \"HLA-*01:01,HLA-*01:01\" default, returned matrix filtered exclude: positions input genotypes allele positions identical previous positions","code":""},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"","code":"DRB1_file <- file.path( \"https://github.com/ANHIG/IMGTHLA/raw\", \"5f2c562056f8ffa89aeea0631f2a52300ee0de17\", \"alignments/DRB1_prot.txt\" ) a <- read_alignments(DRB1_file) genotypes <- c( \"DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02\", \"DRB1*04:174,DRB1*15:152\", \"DRB1*04:56:02,DRB1*15:01:48\", \"DRB1*14:172,DRB1*04:160\", \"DRB1*04:359,DRB1*04:284:02\" ) dosage <- dosage(genotypes, a$onehot) dosage[,1:5] #> posn29_unk posn29_M pos6_R #> DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02 1 2 3 #> DRB1*04:174,DRB1*15:152 2 0 2 #> DRB1*04:56:02,DRB1*15:01:48 2 0 2 #> DRB1*14:172,DRB1*04:160 2 0 2 #> DRB1*04:359,DRB1*04:284:02 2 0 2 #> pos9_E pos9_W #> DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02 3 0 #> DRB1*04:174,DRB1*15:152 1 1 #> DRB1*04:56:02,DRB1*15:01:48 1 1 #> DRB1*14:172,DRB1*04:160 2 0 #> DRB1*04:359,DRB1*04:284:02 2 0"},{"path":"https://slowkow.github.io/hlabud/reference/get_hlabud_dir.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","title":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","text":"function : Get folder name getOption(\"hlabud_dir\") else automatically choose appropriate folder operating system thanks rappdirs. Create folder automatically already exist. Set hlabud_dir option new folder.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/get_hlabud_dir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","text":"","code":"get_hlabud_dir()"},{"path":"https://slowkow.github.io/hlabud/reference/get_hlabud_dir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","text":"name folder.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/get_hlabud_dir.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","text":"locations hlabud_dir folder operating system. Linux: Mac: Windows: set hlabud_dir option, please use:","code":"~/.local/share/hlabud ~/Library/Application Support/hlabud C:\\Documents and Settings\\{User}\\Application Data\\slowkow\\hlabud options(hlabud_dir = \"/my/favorite/path\")"},{"path":"https://slowkow.github.io/hlabud/reference/get_hlabud_dir.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","text":"","code":"if (FALSE) { hlabud_dir <- get_hlabud_dir() }"},{"path":"https://slowkow.github.io/hlabud/reference/get_onehot.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a one-hot encoded matrix from a dataframe of amino acid\nsequences. — get_onehot","title":"Make a one-hot encoded matrix from a dataframe of amino acid\nsequences. — get_onehot","text":"Make one-hot encoded matrix dataframe amino acid sequences.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/get_onehot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a one-hot encoded matrix from a dataframe of amino acid\nsequences. — get_onehot","text":"","code":"get_onehot(al, n_pre)"},{"path":"https://slowkow.github.io/hlabud/reference/get_onehot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a one-hot encoded matrix from a dataframe of amino acid\nsequences. — get_onehot","text":"al dataframe columns allele, seq n_pre number amino acid sequences position 1.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_alignments.html","id":null,"dir":"Reference","previous_headings":"","what":"Get sequence alignments from IMGTHLA — hla_alignments","title":"Get sequence alignments from IMGTHLA — hla_alignments","text":"conventions used alignments (EBI IMGT-HLA help page): entry allele displayed respect reference sequences. identity reference sequence present base displayed hyphen (-). Non-identity reference sequence shown displaying appropriate base position. insertion deletion occurred represented period (.). sequence unknown point alignment, represented asterisk (*). protein alignments null alleles, 'Stop' codons represented hash (X). protein alignments, sequence following termination codon, marked appear blank. conventions used nucleotide protein alignments.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_alignments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get sequence alignments from IMGTHLA — hla_alignments","text":"","code":"hla_alignments( gene = \"DRB1\", type = \"prot\", release = \"latest\", verbose = FALSE )"},{"path":"https://slowkow.github.io/hlabud/reference/hla_alignments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get sequence alignments from IMGTHLA — hla_alignments","text":"gene name gene like \"DRB1\" type type sequence, one \"prot\", \"nuc\", \"gen\" release Default \"latest\". release name like \"3.51.0\". verbose TRUE, print messages along way.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_alignments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get sequence alignments from IMGTHLA — hla_alignments","text":"list dataframe called sequences two matrices alleles onehot. dataframe two columns: allele: name allele, e.g., DQB*01:01 seq: amino acid sequence matrix alleles one row allele, one column position, values representing residues position allele. matrix onehot one-hot encoding variants distinguish alleles, one row allele one column amino acid position.","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/hla_alignments.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get sequence alignments from IMGTHLA — hla_alignments","text":"","code":"# \\donttest{ a <- hla_alignments(\"DRB1\") head(a$sequences) #> # A tibble: 6 × 2 #> allele seq #> #> 1 DRB1*01:01:01:01 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVR.LLERC… #> 2 DRB1*01:01:01:02 ------------------------------------------------------.-----… #> 3 DRB1*01:01:01:03 ------------------------------------------------------.-----… #> 4 DRB1*01:01:01:04 ------------------------------------------------------.-----… #> 5 DRB1*01:01:01:05 ------------------------------------------------------.-----… #> 6 DRB1*01:01:01:06 ------------------------------------------------------.-----… a$alleles[1:6,1:6] #> posn29 posn28 posn27 posn26 posn25 posn24 #> DRB1*01:01:01:01 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" #> DRB1*01:01:01:02 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" #> DRB1*01:01:01:03 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" #> DRB1*01:01:01:04 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" #> DRB1*01:01:01:05 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" #> DRB1*01:01:01:06 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" a$onehot[1:6,1:6] #> posn29_unk posn29_M posn28_unk posn28_L posn28_V posn27_unk #> DRB1*01:01:01:01 0 1 0 0 1 0 #> DRB1*01:01:01:02 0 1 0 0 1 0 #> DRB1*01:01:01:03 0 1 0 0 1 0 #> DRB1*01:01:01:04 0 1 0 0 1 0 #> DRB1*01:01:01:05 0 1 0 0 1 0 #> DRB1*01:01:01:06 0 1 0 0 1 0 # }"},{"path":"https://slowkow.github.io/hlabud/reference/hla_alleles.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","title":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","text":"Download list allele names HLA genes particular IMGTHLA release.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_alleles.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","text":"","code":"hla_alleles(release = \"latest\", overwrite = FALSE, verbose = FALSE)"},{"path":"https://slowkow.github.io/hlabud/reference/hla_alleles.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","text":"release Default \"latest\". release name like \"3.51.0\". overwrite Overwrite existing alleles.json file Allelelist.{version}.txt file verbose TRUE, print messages along way.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_alleles.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","text":"data frame HLA allele ids names","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/hla_alleles.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","text":"","code":"# \\donttest{ head(hla_alleles()) #> AlleleID Allele #> 1 HLA00001 A*01:01:01:01 #> 2 HLA02169 A*01:01:01:02N #> 3 HLA14798 A*01:01:01:03 #> 4 HLA15760 A*01:01:01:04 #> 5 HLA16415 A*01:01:01:05 #> 6 HLA16417 A*01:01:01:06 # }"},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate HLA divergence for each individual — hla_divergence","title":"Calculate HLA divergence for each individual — hla_divergence","text":"First, convert allele name (e.g. *01:01) amino acid sequence. divergence sum distances pair amino acids position, divided total sequence length. amino acid distance matrix use one published Grantham 1974 (doi:10.1126/science.185.4154.862), based three physical properties amino acids (composition, polarity, molecular volume) correlated estimate relative substitution frequency.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate HLA divergence for each individual — hla_divergence","text":"","code":"hla_divergence( alleles = c(\"A*01:01,A*02:01\"), method = \"grantham\", release = \"latest\" )"},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate HLA divergence for each individual — hla_divergence","text":"alleles character vector comma-delimited alleles individual. usually expect two alleles per individual, possible (fewer) copies due copy number alterations. function still works individual different number alleles. method pairwise amino acid matrix, method name: \"grantham\" \"uniform\" indicate pairwise amino acid distance matrix use. choose pass matrix, 20x20 symmetric matrix zeros diagonal, rownames colnames one-letter amino acid codes R N D C Q E G H L K M F P S T W Y V. release Default \"latest\". release name like \"3.51.0\".","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate HLA divergence for each individual — hla_divergence","text":"dataframe divergence individual.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate HLA divergence for each individual — hla_divergence","text":"code function translation original Perl code Tobias Lenz, published Pierini & Lenz 2018 MolBiolEvol (https://doi.org/10.1093/molbev/msy116). comparing two amino acid sequences, characters one 20 amino acids considered divergence calculation, gaps (characters) count.","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate HLA divergence for each individual — hla_divergence","text":"","code":"my_genos <- c(\"A*23:01:12,A*24:550\", \"A*25:12N,A*11:27\", \"A*24:381,A*33:85\", \"A*01:01:,A*01:01,A*02:01\") hla_divergence(my_genos, method = \"grantham\") #> A*23:01:12,A*24:550 A*25:12N,A*11:27 A*24:381,A*33:85 #> 0.4924242 3.3333333 4.9015152 #> A*01:01:,A*01:01,A*02:01 #> 3.8367003 # This is equivalent hla_divergence(my_genos, method = amino_distance_matrix(\"grantham\")) #> A*23:01:12,A*24:550 A*25:12N,A*11:27 A*24:381,A*33:85 #> 0.4924242 3.3333333 4.9015152 #> A*01:01:,A*01:01,A*02:01 #> 3.8367003"},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":null,"dir":"Reference","previous_headings":"","what":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"Download read table HLA allele frequencies Allele Frequency Net Database (AFND).","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"","code":"hla_frequencies(verbose = FALSE)"},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"verbose TRUE, print messages along way.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"dataframe HLA allele frequencies genes.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"use data, please cite latest manuscript Allele Frequency Net Database: Gonzalez-Galarza FF, McCabe , Santos EJMD, Jones J, Takeshita L, Ortega-Rivera ND, et al. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data new query tools. Nucleic Acids Res. 2020;48: D783–D788. doi:10.1093/nar/gkz1029","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"","code":"# \\donttest{ hla_frequencies() #> # A tibble: 123,502 × 7 #> group gene allele population indivs_over_n alleles_over_2n n #> #> 1 hla A A*01:01 Argentina Rosario To… 15.1 0.076 86 #> 2 hla A A*01:01 Armenia combined Reg… NA 0.125 100 #> 3 hla A A*01:01 Australia Cape York … NA 0.053 103 #> 4 hla A A*01:01 Australia Groote Eyl… NA 0.027 75 #> 5 hla A A*01:01 Australia New South … NA 0.187 134 #> 6 hla A A*01:01 Australia Yuendumu A… NA 0.008 191 #> 7 hla A A*01:01 Austria 27 0.146 200 #> 8 hla A A*01:01 Azores Central Islan… NA 0.08 59 #> 9 hla A A*01:01 Azores Oriental Isla… NA 0.115 43 #> 10 hla A A*01:01 Azores Terceira Isla… NA 0.109 130 #> # ℹ 123,492 more rows # }"},{"path":"https://slowkow.github.io/hlabud/reference/hla_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get HLA gene names from IMGTHLA — hla_genes","title":"Get HLA gene names from IMGTHLA — hla_genes","text":"Retrieve list txt files github.com/ANHIG/IMGTHLA/alignments return list gene names derived file names.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get HLA gene names from IMGTHLA — hla_genes","text":"","code":"hla_genes(release = \"latest\", overwrite = FALSE, verbose = FALSE)"},{"path":"https://slowkow.github.io/hlabud/reference/hla_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get HLA gene names from IMGTHLA — hla_genes","text":"release Default \"latest\". release name like \"3.51.0\". overwrite Overwrite existing genes.json file new one GitHub verbose TRUE, print messages along way.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get HLA gene names from IMGTHLA — hla_genes","text":"tibble two columns: HLA gene names (\"\", \"DRB1\") types (\"nuc\", \"gen\", \"prot\").","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/hla_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get HLA gene names from IMGTHLA — hla_genes","text":"","code":"# \\donttest{ hla_genes() #> # A tibble: 107 × 2 #> gene type #> #> 1 A gen #> 2 A nuc #> 3 A prot #> 4 B gen #> 5 B nuc #> 6 B prot #> 7 C gen #> 8 C nuc #> 9 C prot #> 10 DMA gen #> # ℹ 97 more rows # }"},{"path":"https://slowkow.github.io/hlabud/reference/hla_releases.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the names of releases from IMGTHLA — hla_releases","title":"Get the names of releases from IMGTHLA — hla_releases","text":"Get tags github.com/ANHIG/IMGTHLA, save file called tags.json getOption(\"hlabud_dir\"), return release names file.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_releases.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the names of releases from IMGTHLA — hla_releases","text":"","code":"hla_releases(overwrite = FALSE)"},{"path":"https://slowkow.github.io/hlabud/reference/hla_releases.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the names of releases from IMGTHLA — hla_releases","text":"overwrite Overwrite existing tags.json file getOption(\"hlabud_dir\")","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_releases.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the names of releases from IMGTHLA — hla_releases","text":"character vector release names like \"3.51.0\"","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_releases.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the names of releases from IMGTHLA — hla_releases","text":"","code":"# \\donttest{ hla_releases() #> [1] \".354.0\" \"3.53.0\" \"3.52.0\" \"3.51.0\" \"3.50.0\" \"3.49.0\" #> [7] \"3.48.0\" \"3.47.0\" \"3.46.0\" \"3.45.1\" \"3.45.01\" \"3.45.0.1\" #> [13] \"3.45.0\" \"3.44.1\" \"3.44.0\" \"3.43.0\" \"3.42.0\" \"3.41.2\" #> [19] \"3.41.0\" \"3.40.0\" \"3.39.0\" \"3.38.0\" \"3.37.0\" \"3.36.0\" #> [25] \"3.35.0\" \"3.34.0\" \"3.33.0\" \"3.32.0\" \"3.31.0\" \"3.30.0\" # }"},{"path":"https://slowkow.github.io/hlabud/reference/hlabud-package.html","id":null,"dir":"Reference","previous_headings":"","what":"hlabud: Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA — hlabud-package","title":"hlabud: Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA — hlabud-package","text":"Fetch sequence alignment data IMGTHLA database Robinson et al (2020) doi:10.1093/nar/gkz950 , automatically convert sequence alignments convenient R matrices ready downstream analysis. vignette shows examples using one-hot encoding data logistic regression dimensionality reduction. Data downloaded lazily, -needed, cached user-configurable folder.","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/hlabud-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"hlabud: Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA — hlabud-package","text":"Maintainer: Kamil Slowikowski kslowikowski@gmail.com (ORCID)","code":""},{"path":"https://slowkow.github.io/hlabud/reference/install_hla.html","id":null,"dir":"Reference","previous_headings":"","what":"Download and unpack a tarball release from IMGTHLA — install_hla","title":"Download and unpack a tarball release from IMGTHLA — install_hla","text":"release tarball Github unpacked getOption(\"hlabud_dir\") folder.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/install_hla.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download and unpack a tarball release from IMGTHLA — install_hla","text":"","code":"install_hla(release = \"latest\", overwrite = FALSE, verbose = FALSE)"},{"path":"https://slowkow.github.io/hlabud/reference/install_hla.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download and unpack a tarball release from IMGTHLA — install_hla","text":"release Default \"latest\". release name like \"3.51.0\". overwrite TRUE, overwrite existing files release folder. verbose TRUE, print messages along way.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/install_hla.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Download and unpack a tarball release from IMGTHLA — install_hla","text":"Note latest releases 100 MB size, download might take slow connections.","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/install_hla.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download and unpack a tarball release from IMGTHLA — install_hla","text":"","code":"if (FALSE) { install_hla() install_hla(\"3.51.0\") install_hla(\"3.51.0\", verbose = TRUE) # Change the install directory options(hlabud_dir = \"path/to/my/dir\") install_hla() }"},{"path":"https://slowkow.github.io/hlabud/reference/one_to_three.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert one letter amino acid codes to three letter amino acid codes — one_to_three","title":"Convert one letter amino acid codes to three letter amino acid codes — one_to_three","text":"Convert one letter amino acid codes three letter amino acid codes","code":""},{"path":"https://slowkow.github.io/hlabud/reference/one_to_three.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert one letter amino acid codes to three letter amino acid codes — one_to_three","text":"","code":"one_to_three(aminos)"},{"path":"https://slowkow.github.io/hlabud/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling rhs(lhs).","code":""},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":null,"dir":"Reference","previous_headings":"","what":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"function reads txt files provided IMGTHLA.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"","code":"read_alignments(file)"},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"file File name txt file IMGTHLA like \"DQB1_prot.txt\"","code":""},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"list dataframe called sequences two matrices alleles onehot. dataframe two columns: allele: name allele, e.g., DQB*01:01 seq: amino acid sequence matrix alleles one row allele, one column position, values representing residues position allele. matrix onehot one-hot encoding variants distinguish alleles, one row allele one column amino acid position.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"Consider using hla_alignments() instead function. already txt file want read, can read read_alignments(\"myfile.txt\"). sequences contained file: {gene}_prot.txt amino acid sequence HLA allele. {gene}_nuc.txt nucleotide sequence exons. {gene}_gen.txt genomic sequence exons introns.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"","code":"my_file <- file.path( \"https://github.com/ANHIG/IMGTHLA/raw\", \"5f2c562056f8ffa89aeea0631f2a52300ee0de17\", \"alignments/DRB1_prot.txt\" ) a <- read_alignments(my_file) head(a$sequences) #> # A tibble: 6 × 2 #> allele seq #> #> 1 DRB1*01:01:01:01 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVR.LLERC… #> 2 DRB1*01:01:01:02 ------------------------------------------------------.-----… #> 3 DRB1*01:01:01:03 ------------------------------------------------------.-----… #> 4 DRB1*01:01:01:04 ------------------------------------------------------.-----… #> 5 DRB1*01:01:01:05 ------------------------------------------------------.-----… #> 6 DRB1*01:01:01:06 ------------------------------------------------------.-----… a$alleles[1:5,1:5] #> posn29 posn28 posn27 posn26 posn25 #> DRB1*01:01:01:01 \"M\" \"V\" \"C\" \"L\" \"K\" #> DRB1*01:01:01:02 \"M\" \"V\" \"C\" \"L\" \"K\" #> DRB1*01:01:01:03 \"M\" \"V\" \"C\" \"L\" \"K\" #> DRB1*01:01:01:04 \"M\" \"V\" \"C\" \"L\" \"K\" #> DRB1*01:01:01:05 \"M\" \"V\" \"C\" \"L\" \"K\" a$onehot[1:5,1:5] #> posn29_unk posn29_M posn28_unk posn28_V posn27_unk #> DRB1*01:01:01:01 0 1 0 1 0 #> DRB1*01:01:01:02 0 1 0 1 0 #> DRB1*01:01:01:03 0 1 0 1 0 #> DRB1*01:01:01:04 0 1 0 1 0 #> DRB1*01:01:01:05 0 1 0 1 0"},{"path":"https://slowkow.github.io/hlabud/news/index.html","id":"hlabud-1009999","dir":"Changelog","previous_headings":"","what":"hlabud 1.0.0.9999","title":"hlabud 1.0.0.9999","text":"Instead discarding positions *, include label unk, example pos241_unk indicates unknown amino acid position 241. Thanks Sreekar Mantena reporting issue! Fix --one error. example, HLA-pos361_- colnames($onehot) reference allele instead -. now fixed. Thanks Sreekar Mantena reporting issue!","code":""},{"path":"https://slowkow.github.io/hlabud/news/index.html","id":"hlabud-100","dir":"Changelog","previous_headings":"","what":"hlabud 1.0.0","title":"hlabud 1.0.0","text":"Added NEWS.md file track changes package.","code":""}]
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Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"hlabud usage examples","text":"Kamil Slowikowski 2023-11-29 hlabud R package provides functions facilitate download analysis human leukocyte antigen (HLA) genotype sequence alignments IMGTHLA R. Let’s consider question might want answer HLA genotypes. amino acid positions different DRB1*04:174 DRB1*15:152 genotypes? hlabud, can find answer lines code: two genotypes nearly identical, amino acid position 9 different: position 9 E (Glu) DRB1*04:174 position 9 W (Trp) DRB1*15:152 just easy find nucleotides distinguish two alleles:","code":"library(hlabud) a <- hla_alignments(\"DRB1\") dosage(c(\"DRB1*04:174\", \"DRB1*15:152\"), a$onehot) #> pos9_E pos9_W #> DRB1*04:174 1 0 #> DRB1*15:152 0 1 n <- hla_alignments(\"DRB1\", type = \"nuc\") dosage(c(\"DRB1*04:174\", \"DRB1*15:152\"), n$onehot) #> pos109_C pos109_T #> DRB1*04:174 0 1 #> DRB1*15:152 1 0"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"hlabud usage examples","text":"quickest way get hlabud install GitHub: , included usage examples. hope inspire share HLA analyses. source code page available . Thank reporting issues hlabud.","code":"# install.packages(\"devtools\") devtools::install_github(\"slowkow/hlabud\")"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"get-a-one-hot-encoded-matrix-for-all-hla-drb1-alleles","dir":"Articles","previous_headings":"","what":"Get a one-hot encoded matrix for all HLA-DRB1 alleles","title":"hlabud usage examples","text":"can use hla_alignments(\"DRB1\") load DRB1_prot.txt file latest IMGTHLA release: object list three items: $sequences amino acid sequence alignments data frame: conventions used alignments (copied EBI): entry allele displayed respect reference sequences. identity reference sequence present base displayed hyphen (-). Non-identity reference sequence shown displaying appropriate base position. insertion deletion occurred represented period (.). sequence unknown point alignment, represented asterisk (*). protein alignments null alleles, ‘Stop’ codons represented hash (X). protein alignments, sequence following termination codon, marked appear blank. conventions used nucleotide protein alignments. Learn alignments : https://www.ebi.ac.uk/ipd/imgt/hla/alignment/help/ $alleles matrix amino acids one column position: $onehot one-hot encoded matrix one column amino acid position:","code":"library(hlabud) a <- hla_alignments(gene = \"DRB1\", verbose = TRUE) #> Reading /home/runner/.local/share/hlabud/.354.0/alignments/DRB1_prot.txt str(a) #> List of 3 #> $ sequences: tibble [3,588 × 2] (S3: tbl_df/tbl/data.frame) #> ..$ allele: chr [1:3588] \"DRB1*01:01:01:01\" \"DRB1*01:01:01:02\" \"DRB1*01:01:01:03\" \"DRB1*01:01:01:04\" ... #> ..$ seq : chr [1:3588] \"MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVR.LLERCIYNQEE.SVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCR\"| __truncated__ \"------------------------------------------------------.-----------.--------------------------------------------\"| __truncated__ \"------------------------------------------------------.-----------.--------------------------------------------\"| __truncated__ \"------------------------------------------------------.-----------.--------------------------------------------\"| __truncated__ ... #> $ alleles : chr [1:3588, 1:288] \"M\" \"M\" \"M\" \"M\" ... #> ..- attr(*, \"dimnames\")=List of 2 #> .. ..$ : chr [1:3588] \"DRB1*01:01:01:01\" \"DRB1*01:01:01:02\" \"DRB1*01:01:01:03\" \"DRB1*01:01:01:04\" ... #> .. ..$ : chr [1:288] \"posn29\" \"posn28\" \"posn27\" \"posn26\" ... #> $ onehot : num [1:3588, 1:1786] 0 0 0 0 0 0 0 0 0 0 ... #> ..- attr(*, \"dimnames\")=List of 2 #> .. ..$ : chr [1:3588] \"DRB1*01:01:01:01\" \"DRB1*01:01:01:02\" \"DRB1*01:01:01:03\" \"DRB1*01:01:01:04\" ... #> .. ..$ : chr [1:1786] \"posn29_unk\" \"posn29_M\" \"posn28_unk\" \"posn28_L\" ... a$sequences #> # A tibble: 3,588 × 2 #> allele seq #> #> 1 DRB1*01:01:01:01 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVR.LLER… #> 2 DRB1*01:01:01:02 ------------------------------------------------------.----… #> 3 DRB1*01:01:01:03 ------------------------------------------------------.----… #> 4 DRB1*01:01:01:04 ------------------------------------------------------.----… #> 5 DRB1*01:01:01:05 ------------------------------------------------------.----… #> 6 DRB1*01:01:01:06 ------------------------------------------------------.----… #> 7 DRB1*01:01:01:07 ------------------------------------------------------.----… #> 8 DRB1*01:01:01:08 ------------------------------------------------------.----… #> 9 DRB1*01:01:01:09 ------------------------------------------------------.----… #> 10 DRB1*01:01:01:10 ------------------------------------------------------.----… #> # ℹ 3,578 more rows a$alleles[1:5,1:7] #> posn29 posn28 posn27 posn26 posn25 posn24 posn23 #> DRB1*01:01:01:01 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" \"P\" #> DRB1*01:01:01:02 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" \"P\" #> DRB1*01:01:01:03 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" \"P\" #> DRB1*01:01:01:04 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" \"P\" #> DRB1*01:01:01:05 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" \"P\" a$onehot[1:5,1:7] #> posn29_unk posn29_M posn28_unk posn28_L posn28_V posn27_unk #> DRB1*01:01:01:01 0 1 0 0 1 0 #> DRB1*01:01:01:02 0 1 0 0 1 0 #> DRB1*01:01:01:03 0 1 0 0 1 0 #> DRB1*01:01:01:04 0 1 0 0 1 0 #> DRB1*01:01:01:05 0 1 0 0 1 0 #> posn27_C #> DRB1*01:01:01:01 1 #> DRB1*01:01:01:02 1 #> DRB1*01:01:01:03 1 #> DRB1*01:01:01:04 1 #> DRB1*01:01:01:05 1"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"convert-genotypes-to-a-dosage-matrix","dir":"Articles","previous_headings":"","what":"Convert genotypes to a dosage matrix","title":"hlabud usage examples","text":"Suppose individuals following genotypes: want run association test amino acid positions, need convert genotype names matrix allele dosages (e.g., 0, 1, 2). can use dosage() convert individual’s genotypes amino acid dosages: Note: dosage matrix one row individual one column amino acid position. default, dosage() discard columns individuals identical. first individual dosage=3 pos6_R (position 6 Arg). ’s assigned individual 3 alleles input. Please careful check data looks way expect!","code":"genotypes <- c( \"DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02\", \"DRB1*04:174,DRB1*15:152\", \"DRB1*04:56:02,DRB1*15:01:48\", \"DRB1*14:172,DRB1*04:160\", \"DRB1*04:359,DRB1*04:284:02\" ) dosage <- dosage(genotypes, a$onehot) dosage[,1:4] #> posn29_unk posn29_M pos6_R #> DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02 1 2 3 #> DRB1*04:174,DRB1*15:152 2 0 2 #> DRB1*04:56:02,DRB1*15:01:48 2 0 2 #> DRB1*14:172,DRB1*04:160 2 0 2 #> DRB1*04:359,DRB1*04:284:02 2 0 2 #> pos9_E #> DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02 3 #> DRB1*04:174,DRB1*15:152 1 #> DRB1*04:56:02,DRB1*15:01:48 1 #> DRB1*14:172,DRB1*04:160 2 #> DRB1*04:359,DRB1*04:284:02 2 dim(dosage) #> [1] 5 38"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"logistic-regression-association-for-amino-acid-positions","dir":"Articles","previous_headings":"","what":"Logistic regression association for amino acid positions","title":"hlabud usage examples","text":"Let’s simulate dataset cases controls demonstrate one approach testing amino acid positions might associated cases. simulated dataset 100 individuals, 52 cases 48 controls. also one column amino acid position might want test association case variable. One possible approach association testing use glm() fit logistic regression model amino acid position. reveal amino acid position might associated case variable simulated dataset. volcano shows Odds Ratio P-value amino acid position. top hits P < 0.05 labeled. simulation, case variable associated pos123_S (P = 0.026, = 0.52, 95% CI 0.28 0.91).","code":"set.seed(2) n <- 100 d <- data.frame( geno = paste( sample(rownames(a$onehot), n, replace = TRUE), sample(rownames(a$onehot), n, replace = TRUE), sep = \",\" ), age = sample(21:100, n, replace = TRUE), case = sample(0:1, n, replace = TRUE) ) d <- cbind(d, dosage(d$geno, a$onehot)) d[1:5,1:6] #> geno age case #> DRB1*04:256,DRB1*04:125 DRB1*04:256,DRB1*04:125 55 0 #> DRB1*04:11:01:02,DRB1*01:02:12 DRB1*04:11:01:02,DRB1*01:02:12 73 1 #> DRB1*14:08,DRB1*15:01:02 DRB1*14:08,DRB1*15:01:02 72 0 #> DRB1*03:90,DRB1*04:278 DRB1*03:90,DRB1*04:278 22 1 #> DRB1*03:67N,DRB1*03:100:02 DRB1*03:67N,DRB1*03:100:02 34 0 #> posn29_unk posn29_M posn25_K #> DRB1*04:256,DRB1*04:125 2 0 0 #> DRB1*04:11:01:02,DRB1*01:02:12 1 1 1 #> DRB1*14:08,DRB1*15:01:02 0 2 1 #> DRB1*03:90,DRB1*04:278 2 0 0 #> DRB1*03:67N,DRB1*03:100:02 2 0 0 # select the amino acid positions that have at least 3 people with dosage > 0 my_as <- names(which(colSums(d[,4:ncol(d)] > 0) >= 3)) # run the association tests my_glm <- rbindlist(pblapply(my_as, function(my_a) { f <- sprintf(\"case ~ %s\", my_a) glm(as.formula(f), data = d, family = \"binomial\") %>% parameters(exponentiate = TRUE) })) # look at the top hits my_glm %>% arrange(p) %>% filter(!Parameter %in% c(\"(Intercept)\")) %>% head #> Parameter Coefficient SE CI CI_low CI_high z #> 1: pos123_S 0.5161604 0.1528830 0.95 0.282671869 0.9100318 -2.232794 #> 2: pos183_V 0.5570074 0.1572414 0.95 0.314570198 0.9582010 -2.072913 #> 3: pos34_H 2.1982280 0.8658531 0.95 1.053839944 5.0273874 1.999690 #> 4: pos51_A 0.1170213 0.1265210 0.95 0.006179376 0.6749415 -1.984314 #> 5: pos107_S 0.5815232 0.1638237 0.95 0.329174623 1.0003310 -1.924302 #> 6: pos69_L 1.6740699 0.4630002 0.95 0.982434872 2.9247856 1.863017 #> df_error p #> 1: Inf 0.02556252 #> 2: Inf 0.03818041 #> 3: Inf 0.04553374 #> 4: Inf 0.04722090 #> 5: Inf 0.05431680 #> 6: Inf 0.06245981"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"umap-embedding-of-3588-hla-drb1-alleles","dir":"Articles","previous_headings":"","what":"UMAP embedding of 3,588 HLA-DRB1 alleles","title":"hlabud usage examples","text":"many possibilities analysis one-hot encoding HLA-DRB1 alleles. example, UMAP embedding 3,588 HLA-DRB1 alleles encoded one-hot amino acid matrix 1786 columns, one amino acid position. can highlight alleles amino acid H position 13: can represent amino acid position 13 different color:","code":"uamp(a$onehot, n_epochs = 200, min_dist = 1, spread = 2)"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"get-hla-allele-frequencies-from-allele-frequency-net-database-afnd","dir":"Articles","previous_headings":"","what":"Get HLA allele frequencies from Allele Frequency Net Database (AFND)","title":"hlabud usage examples","text":"Download read table HLA allele frequencies Allele Frequency Net Database (AFND). use data, please cite latest manuscript Allele Frequency Net Database: Gonzalez-Galarza FF, McCabe , Santos EJMD, Jones J, Takeshita L, Ortega-Rivera ND, et al. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data new query tools. Nucleic Acids Res. 2020;48: D783–D788. doi:10.1093/nar/gkz1029 Plot frequency specific allele (DQB1*02:01) populations 1000 sampled individuals: See github.com/slowkow/allelefrequencies examples might use data.","code":"af <- hla_frequencies() af #> # A tibble: 123,502 × 7 #> group gene allele population indivs_over_n alleles_over_2n n #> #> 1 hla A A*01:01 Argentina Rosario To… 15.1 0.076 86 #> 2 hla A A*01:01 Armenia combined Reg… NA 0.125 100 #> 3 hla A A*01:01 Australia Cape York … NA 0.053 103 #> 4 hla A A*01:01 Australia Groote Eyl… NA 0.027 75 #> 5 hla A A*01:01 Australia New South … NA 0.187 134 #> 6 hla A A*01:01 Australia Yuendumu A… NA 0.008 191 #> 7 hla A A*01:01 Austria 27 0.146 200 #> 8 hla A A*01:01 Azores Central Islan… NA 0.08 59 #> 9 hla A A*01:01 Azores Oriental Isla… NA 0.115 43 #> 10 hla A A*01:01 Azores Terceira Isla… NA 0.109 130 #> # ℹ 123,492 more rows my_allele <- \"DQB1*02:01\" my_af <- af %>% filter(allele == my_allele) %>% filter(n > 1000) %>% arrange(-alleles_over_2n) ggplot(my_af) + aes(x = alleles_over_2n, y = reorder(population, alleles_over_2n)) + scale_y_discrete(position = \"right\") + geom_colh() + labs( x = \"Allele Frequency (Alleles / 2N)\", y = NULL, title = glue(\"Frequency of {my_allele} across {length(unique(my_af$population))} populations\"), caption = \"Data from AFND http://allelefrequencies.net\" )"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"compute-hla-divergence-with-the-grantham-distance-matrix","dir":"Articles","previous_headings":"","what":"Compute HLA divergence with the Grantham distance matrix","title":"hlabud usage examples","text":"HLA allele binds specific set peptides. , individual two highly dissimilar alleles can bind greater number different peptides homozygous individual (https://doi.org/10.1007/BF02918202): MHC class II allele capacity bind present specific set peptides processed antigens. inability specific class II allele bind present fragment derived processed antigen results loss immune responsiveness antigen individuals homozygous class II allele. can compute HLA divergence metric set individuals like : divergence homozygote equal zero, definition: default, use amino acid distance matrix Granthan 1974 (https://doi.org/10.1126/science.185.4154.862). Alternatively, can choose use uniform matrix instead (diagonal values 0, non-diagonal values equal 1): amino acid distance matrix easily accessible, provide two built-options \"grantham\" \"uniform\":","code":"my_genos <- c(\"A*23:01:12,A*24:550\", \"A*25:12N,A*11:27\", \"A*24:381,A*33:85\") hla_divergence(my_genos, method = \"grantham\") #> A*23:01:12,A*24:550 A*25:12N,A*11:27 A*24:381,A*33:85 #> 0.4924242 3.3333333 4.9015152 hla_divergence(\"A*01:01,A*01:01\") #> A*01:01,A*01:01 #> 0 hla_divergence(my_genos, method = \"uniform\") #> A*23:01:12,A*24:550 A*25:12N,A*11:27 A*24:381,A*33:85 #> 0.007575758 0.040404040 0.060606061 amino_distance_matrix(method = \"uniform\") #> A R N D C Q E G H I L K M F P S T W Y V #> A 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> R 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> N 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> D 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> C 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> Q 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> E 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 #> G 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 #> H 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 #> I 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 #> L 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 #> K 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 #> M 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 #> F 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 #> P 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 #> S 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 #> T 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 #> W 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 #> Y 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 #> V 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"download-and-unpack-all-data-from-the-latest-imgthla-release","dir":"Articles","previous_headings":"","what":"Download and unpack all data from the latest IMGTHLA release","title":"hlabud usage examples","text":"want use hla_alignments(), don’t need install_hla() data files downloaded automatically needed cached future use. users might need access additional files present full data release. Run install_hla() download unpack latest IMGTHLA release. destination folder downloaded data files getOption(\"hlabud_dir\") (automatically tailored operating system thanks rappdirs package). examples download releases get list release names. Download latest release (default) specific release: Optionally, get set directory hlabud uses store data: List releases: installing releases, hlabud folder might look like :","code":"# Download all of the data (120MB) for the latest IMGTHLA release install_hla(release = \"latest\") # Download a specific release install_hla(release = \"3.51.0\") getOption(\"hlabud_dir\") #> [1] \"/home/username/.local/share/hlabud\" # Manually override the directory for hlabud to use options(hlabud_dir = \"/path/to/my/dir\") hla_releases() #> [1] \"3.51.0\" \"3.50.0\" \"3.49.0\" \"3.48.0\" \"3.47.0\" \"3.46.0\" \"3.45.1\" \"3.45.01\" #> [9] \"3.45.0.1\" \"3.45.0\" \"3.44.1\" \"3.44.0\" \"3.43.0\" \"3.42.0\" \"3.41.2\" \"3.41.0\" #> [17] \"3.40.0\" \"3.39.0\" \"3.38.0\" \"3.37.0\" \"3.36.0\" \"3.35.0\" \"3.34.0\" \"3.33.0\" #> [25] \"3.32.0\" \"3.31.0\" \"3.30.0\" \"3.29.0\" \"3.28.0\" \"3.27.0\" ❯ ls -lah \"/home/user/.local/share/hlabud\" total 207M drwxrwxr-x 3 user user 32 Apr 5 01:19 3.30.0 drwxrwxr-x 11 user user 4.0K Apr 7 19:31 3.40.0 drwxrwxr-x 12 user user 4.0K Apr 5 00:27 3.51.0 -rw-rw-r-- 1 user user 15K Apr 7 19:23 tags.json -rw-rw-r-- 1 user user 79M Apr 7 19:28 v3.40.0-alpha.tar.gz -rw-rw-r-- 1 user user 129M Apr 4 20:07 v3.51.0-alpha.tar.gz"},{"path":"https://slowkow.github.io/hlabud/articles/examples.html","id":"count-the-number-of-alleles-in-each-imgthla-release","dir":"Articles","previous_headings":"","what":"Count the number of alleles in each IMGTHLA release","title":"hlabud usage examples","text":"can get list release names: can get allele names release: Next, count many alleles release: plot number alleles line plot:","code":"releases <- hla_releases() releases #> [1] \".354.0\" \"3.53.0\" \"3.52.0\" \"3.51.0\" \"3.50.0\" \"3.49.0\" #> [7] \"3.48.0\" \"3.47.0\" \"3.46.0\" \"3.45.1\" \"3.45.01\" \"3.45.0.1\" #> [13] \"3.45.0\" \"3.44.1\" \"3.44.0\" \"3.43.0\" \"3.42.0\" \"3.41.2\" #> [19] \"3.41.0\" \"3.40.0\" \"3.39.0\" \"3.38.0\" \"3.37.0\" \"3.36.0\" #> [25] \"3.35.0\" \"3.34.0\" \"3.33.0\" \"3.32.0\" \"3.31.0\" \"3.30.0\" my_alleles <- rbindlist(lapply(releases, function(release) { retval <- hla_alleles(release = release) retval$release <- release return(retval) }), fill = TRUE) #> Warning in hla_alleles(release = release): unrecognized release name #> 'Allelelist.3451.txt' #> Warning in hla_alleles(release = release): unrecognized release name #> 'Allelelist.34501.txt' #> Warning in hla_alleles(release = release): unrecognized release name #> 'Allelelist.34501.txt' #> Warning in hla_alleles(release = release): unrecognized release name #> 'Allelelist.3441.txt' #> Warning in hla_alleles(release = release): unrecognized release name #> 'Allelelist.3412.txt' d <- my_alleles %>% count(release) %>% filter(n > 1) d #> release n #> 1: .354.0 38416 #> 2: 3.30.0 17509 #> 3: 3.31.0 17874 #> 4: 3.32.0 18363 #> 5: 3.33.0 18955 #> 6: 3.34.0 20272 #> 7: 3.35.0 21683 #> 8: 3.36.0 22548 #> 9: 3.37.0 24093 #> 10: 3.38.0 25958 #> 11: 3.39.0 26512 #> 12: 3.40.0 27273 #> 13: 3.41.0 27980 #> 14: 3.42.0 28786 #> 15: 3.43.0 29417 #> 16: 3.44.0 30523 #> 17: 3.45.0 31552 #> 18: 3.46.0 32330 #> 19: 3.47.0 33552 #> 20: 3.48.0 34145 #> 21: 3.49.0 35077 #> 22: 3.50.0 36016 #> 23: 3.51.0 36625 #> 24: 3.52.0 37068 #> 25: 3.53.0 37619 #> release n ggplot(d) + aes(x = release, y = n, group = 1) + geom_line() + geom_text(aes(label = release), hjust = 1) + labs(x = NULL, y = \"Number of alleles\", title = \"Each release has more HLA alleles\") + theme( axis.text.x = element_blank(), axis.ticks.x = element_blank(), ) d2 <- my_alleles %>% mutate(gene = str_split_fixed(Allele, \"\\\\*\", 2)[,1]) %>% count(release, gene) ggplot() + aes(x = release, y = n) + geom_line( data = d2, aes(group = gene, color = gene) ) + scale_color_discrete(guide = \"none\") + geom_text( data = d2 %>% filter(release == \"3.52.0\"), mapping = aes(label = gene), hjust = 0 ) + labs(x = NULL, y = \"Number of alleles\", title = \"Number of alleles per release and gene\") + scale_x_discrete(expand = expansion(mult = c(0.01, 0.1))) + scale_y_log10() + theme( panel.grid.major.y = element_line(), axis.text.x = element_blank(), axis.ticks.x = element_blank(), )"},{"path":"https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Visualize HLA protein structures","text":"Kamil Slowikowski 2023-11-29 vignette, explore different methods visualizing molecular structure HLA proteins. First, ’ll look example use NGLVieweR R package show HLA protein structures. Next, ’ll use PyMOL thing.","code":""},{"path":"https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html","id":"what-are-the-pdb-identifiers-for-each-hla-gene","dir":"Articles","previous_headings":"","what":"What are the PDB identifiers for each HLA gene?","title":"Visualize HLA protein structures","text":"list PDB identifiers might consider using represent HLA protein: Also try searching PDB website , e.g., \"HLA-DR\" see appropriate structure analysis.","code":"HLA-A 2xpg HLA-B 2bvp HLA-C 4nt6 HLA-DP 3lqz HLA-DQ 4z7w HLA-DR 3pdo"},{"path":"https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html","id":"using-nglviewer","dir":"Articles","previous_headings":"","what":"Using NGLVieweR","title":"Visualize HLA protein structures","text":"Let’s try visualize position 9 HLA-B protein structure. visualize structure 2bvp Protein Data Bank (PDB). example NGLVieweR R package Niels van der Velden: view , see blue peptide red HLA-B protein. tyrosine position 9 highlighted ball+stick representation, also labeled text label. structure rotating can getter better view. can use hlabud answer questions HLA-B Tyr9 (tyrosine position 9). example, HLA-B alleles amino acid position? fraction reported HLA-B alleles Tyr9?","code":"# devtools::install_github(\"nvelden/NGLVieweR\") # we need the latest version library(NGLVieweR) library(magrittr) my_sele <- \"9:A\" NGLVieweR(\"2bvp\") %>% stageParameters( backgroundColor = \"white\", zoomSpeed = 1, cameraFov = 80 ) %>% addRepresentation( type = \"cartoon\" ) %>% addRepresentation( type = \"ball+stick\", param = list( sele = my_sele ) ) %>% addRepresentation( type = \"label\", param = list( sele = my_sele, labelType = \"format\", labelFormat = \"[%(resname)s]%(resno)s\", # or enter custom text labelGrouping = \"residue\", # or \"atom\" (eg. sele = \"20:A.CB\") color = \"black\", fontFamiliy = \"sans-serif\", xOffset = 1, yOffset = 0, zOffset = 0, fixedSize = TRUE, radiusType = 1, radiusSize = 5.5, # Label size showBackground = TRUE # backgroundColor=\"black\", # backgroundOpacity=0.5 ) ) %>% zoomMove( center = my_sele, zoom = my_sele, duration = 0, # animation time in ms z_offSet = -20 ) %>% setSpin() library(hlabud) a <- hla_alignments(\"B\") head(names(which(a$onehot[,\"pos9_Y\"] == 1))) #> [1] \"B*07:02:01:01\" \"B*07:02:01:02\" \"B*07:02:01:03\" \"B*07:02:01:04\" #> [5] \"B*07:02:01:05\" \"B*07:02:01:06\" sum(a$onehot[,\"pos9_Y\"] == 1) / nrow(a$onehot) #> [1] 0.7101798"},{"path":"https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html","id":"using-pymol","dir":"Articles","previous_headings":"","what":"Using PyMOL","title":"Visualize HLA protein structures","text":"PyMOL one favorite methods visualizing protein structures, allows us change residue existing protein visualize new mutated protein. takes lines PyMOL create nice figure. example, want quickly highlight positions 13 45 HLA-DQB1, snippet PyMOL code produce figure . Bash script : Write PyMOL script Run PyMOL script pymol command PyMOL script : Load structure Protein Data Bank (PDB). 7kei identifier published protein structure. Color HLA-DQA1 protein teal. Color HLA-DQB1 protein orange. Color peptide purple. color residues 13 45 HLA-DQB1 red. Label residues positions names. Write PNG file view structure. image , manually rotated structure mouse added text labels like \"PDB: 7kei\" saving file.","code":"#!/usr/bin/env bash # Write a pymol script cat << EOF > script.pml fetch 7kei show cartoon remove solvent remove chain D remove chain H color teal, chain A color orange, chain B color purple, chain C color red, chain B & resi 13 color red, chain B & resi 45 label n. CA and chain B & resi 13, \"%s %s\" % (resi, resn) label n. CA and chain B & resi 45, \"%s %s\" % (resi, resn) png 7kei.png, width=1200, height=800, dpi=300 EOF # On Linux, we can just use `pymol` without making an alias # On macOS, we need to make an alias alias pymol=/Applications/PyMOL.app/Contents/MacOS/PyMOL pymol -c script.pml"},{"path":"https://slowkow.github.io/hlabud/articles/visualize-hla-structure.html","id":"other-pdb-viewers","dir":"Articles","previous_headings":"","what":"Other PDB viewers","title":"Visualize HLA protein structures","text":"Python: https://github.com/nglviewer/nglview Javascript: https://www.rcsb.org/3d-view https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=7kei&bu=1 https://github.com/nglviewer/ngl https://github.com/biasmv/pv R: https://www.raymolecule.com","code":""},{"path":"https://slowkow.github.io/hlabud/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Kamil Slowikowski. Author, maintainer.","code":""},{"path":"https://slowkow.github.io/hlabud/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"J R, DJ B, X G, MA C, P F, SGE. M (2019). “IPD-IMGT/HLA Database.” Nucleic Acids Research, 48(D1), D948–D955. doi:10.1093/nar/gkz950. Slowikowski K (2023). hlabud: IMGTHLA Data R. doi:10.5281/zenodo.8183949, R package version 1.0.0.9999, https://github.com/slowkow/hlabud.","code":"@Article{, author = {Robinson J and Barker DJ and Georgiou X and Cooper MA and Flicek P and Marsh SGE.}, title = {IPD-IMGT/HLA Database}, doi = {10.1093/nar/gkz950}, year = {2019}, month = {oct}, publisher = {Oxford University Press}, volume = {48}, number = {D1}, pages = {D948–D955}, journal = {Nucleic Acids Research}, } @Manual{, title = {{hlabud}: IMGTHLA Data from R}, author = {Kamil Slowikowski}, year = {2023}, note = {R package version 1.0.0.9999}, doi = {10.5281/zenodo.8183949}, url = {https://github.com/slowkow/hlabud}, }"},{"path":"https://slowkow.github.io/hlabud/index.html","id":"hlabud-hla-analysis-in-r-","dir":"","previous_headings":"","what":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","title":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","text":"hlabud provides methods retrieve sequence alignment data IMGTHLA convert data convenient R matrices ready downstream analysis. See usage examples learn use data logistic regression dimensionality reduction. also share tips visualize 3D molecular structure HLA proteins highlight specific amino acid residues. example, let’s consider simple question two HLA genotypes DRB1*04:174 DRB1*15:152. amino acid positions different two genotypes? output, can conclude two genotypes nearly identical, different amino acids E W position 9.","code":"library(hlabud) a <- hla_alignments(\"DRB1\") dosage(c(\"DRB1*04:174\", \"DRB1*15:152\"), a$onehot) ## pos9_E pos9_W ## DRB1*04:174 1 0 ## DRB1*15:152 0 1"},{"path":"https://slowkow.github.io/hlabud/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","text":"quickest way get hlabud install GitHub:","code":"# install.packages(\"devtools\") devtools::install_github(\"slowkow/hlabud\")"},{"path":"https://slowkow.github.io/hlabud/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","text":"See usage examples get ideas use hlabud analyses. Get one-hot encoded matrix HLA-DRB1 alleles Convert genotypes dosage matrix Logistic regression association amino acid positions UMAP embedding 3,516 HLA-DRB1 alleles Get HLA allele frequencies Allele Frequency Net Database (AFND) Compute HLA divergence Grantham distance matrix Download unpack data latest IMGTHLA release","code":""},{"path":"https://slowkow.github.io/hlabud/index.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","text":"hlabud provides access data IMGT/HLA database. Therefore, use hlabud please cite IMGT/HLA paper: Robinson J, Barker DJ, Georgiou X, Cooper MA, Flicek P, Marsh SGE. IPD-IMGT/HLA Database. Nucleic Acids Res. 2020;48: D948–D955. doi:10.1093/nar/gkz950 hlabud also provides access data Allele Frequency Net Database (AFND). Therefore, use hlabud::hla_frequencies() please cite AFND paper: Gonzalez-Galarza FF, McCabe , Santos EJMD, Jones J, Takeshita L, Ortega-Rivera ND, et al. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data new query tools. Nucleic Acids Res. 2020;48: D783–D788. doi:10.1093/nar/gkz1029 Additionally, can also cite hlabud package like : Slowikowski K. hlabud: methods access analysis human leukocyte antigen (HLA) gene sequence alignments IMGT/HLA. R package version 1.0.0.","code":""},{"path":"https://slowkow.github.io/hlabud/index.html","id":"related-work","dir":"","previous_headings":"","what":"Related work","title":"Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA","text":"recommend article anyone new HLA, beautiful figures help build intuition: La Gruta NL, Gras S, Daley SR, Thomas PG, Rossjohn J. Understanding drivers MHC restriction T cell receptors. Nat Rev Immunol. 2018;18: 467–478. Learn conventions HLA nomenclature: Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, et al. Nomenclature factors HLA system, 2010. Tissue Antigens. 2010;75: 291–455. case-control analysis HLA genotype data, consider BIGDAWG R package available CRAN. related article: Pappas DJ, Marin W, Hollenbach JA, Mack SJ. Bridging ImmunoGenomic Data Analysis Workflow Gaps (BIGDAWG): integrated case-control analysis pipeline. Hum Immunol. 2016;77: 283–287.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/amino_distance_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","title":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","text":"default, return amino acid distance matrix Grantham 1974 (doi:10.1126/science.185.4154.862).","code":""},{"path":"https://slowkow.github.io/hlabud/reference/amino_distance_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","text":"","code":"amino_distance_matrix(method = \"grantham\")"},{"path":"https://slowkow.github.io/hlabud/reference/amino_distance_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","text":"method \"grantham\" Grantham 1974 matrix \"uniform\" matrix ones non-diagonal.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/amino_distance_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","text":"20x20 symmetric matrix positive numbers zeros diagonal.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/amino_distance_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get a pairwise 20x20 distance matrix for all pairs of amino acids — amino_distance_matrix","text":"","code":"# By default, the Grantham 1974 matrix amino_distance_matrix(\"grantham\") #> A R N D C Q E G H I L K M F P S T W Y #> A 0 112 111 126 195 91 107 60 86 94 96 106 84 113 27 99 58 148 112 #> R 112 0 86 96 180 43 54 125 29 97 102 26 91 97 103 110 71 101 77 #> N 111 86 0 23 139 46 42 80 68 149 153 94 142 158 91 46 65 174 143 #> D 126 96 23 0 154 61 45 94 81 168 172 101 160 177 108 65 85 181 160 #> C 195 180 139 154 0 154 170 159 174 198 198 202 196 205 169 112 149 215 194 #> Q 91 43 46 61 154 0 29 87 24 109 113 53 101 116 76 68 42 130 99 #> E 107 54 42 45 170 29 0 98 40 134 138 56 126 140 93 80 65 152 122 #> G 60 125 80 94 159 87 98 0 98 135 138 127 127 153 42 56 59 184 147 #> H 86 29 68 81 174 24 40 98 0 94 99 32 87 100 77 89 47 115 83 #> I 94 97 149 168 198 109 134 135 94 0 5 102 10 21 95 142 89 61 33 #> L 96 102 153 172 198 113 138 138 99 5 0 107 15 22 98 145 92 61 36 #> K 106 26 94 101 202 53 56 127 32 102 107 0 95 102 103 121 78 110 85 #> M 84 91 142 160 196 101 126 127 87 10 15 95 0 28 87 135 81 67 36 #> F 113 97 158 177 205 116 140 153 100 21 22 102 28 0 114 155 103 40 22 #> P 27 103 91 108 169 76 93 42 77 95 98 103 87 114 0 74 38 147 110 #> S 99 110 46 65 112 68 80 56 89 142 145 121 135 155 74 0 58 177 144 #> T 58 71 65 85 149 42 65 59 47 89 92 78 81 103 38 58 0 128 92 #> W 148 101 174 181 215 130 152 184 115 61 61 110 67 40 147 177 128 0 37 #> Y 112 77 143 160 194 99 122 147 83 33 36 85 36 22 110 144 92 37 0 #> V 64 96 133 152 192 96 121 109 84 29 32 97 21 50 68 124 69 88 55 #> V #> A 64 #> R 96 #> N 133 #> D 152 #> C 192 #> Q 96 #> E 121 #> G 109 #> H 84 #> I 29 #> L 32 #> K 97 #> M 21 #> F 50 #> P 68 #> S 124 #> T 69 #> W 88 #> Y 55 #> V 0 # All ones, and zeros on the diagonal amino_distance_matrix(\"uniform\") #> A R N D C Q E G H I L K M F P S T W Y V #> A 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> R 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> N 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> D 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> C 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> Q 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 #> E 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 #> G 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 #> H 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 1 #> I 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 1 #> L 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 1 #> K 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 1 #> M 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 1 #> F 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 1 #> P 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 1 #> S 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 1 #> T 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 1 #> W 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 1 #> Y 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 #> V 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0"},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"genotype name, return dosage matrix residue (amino acid nucleotide) position.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"","code":"dosage(names, mat, drop_constants = TRUE, drop_duplicates = TRUE)"},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"names Input character vector one genotype individual. entries must present rownames(mat). mat one-hot encoded matrix one row per allele one column residue (amino acid nucleotide) position. drop_constants Filter constant amino acid positions default. drop_duplicates Filter duplicate amino acid positions default.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"matrix one row input genotype, one column residue position.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"genotype represented like \"HLA-*01:01,HLA-*01:01\" default, returned matrix filtered exclude: positions input genotypes allele positions identical previous positions","code":""},{"path":"https://slowkow.github.io/hlabud/reference/dosage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert a set of genotype names into a dosage matrix of each residue at each position — dosage","text":"","code":"DRB1_file <- file.path( \"https://github.com/ANHIG/IMGTHLA/raw\", \"5f2c562056f8ffa89aeea0631f2a52300ee0de17\", \"alignments/DRB1_prot.txt\" ) a <- read_alignments(DRB1_file) genotypes <- c( \"DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02\", \"DRB1*04:174,DRB1*15:152\", \"DRB1*04:56:02,DRB1*15:01:48\", \"DRB1*14:172,DRB1*04:160\", \"DRB1*04:359,DRB1*04:284:02\" ) dosage <- dosage(genotypes, a$onehot) dosage[,1:5] #> posn29_unk posn29_M pos6_R #> DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02 1 2 3 #> DRB1*04:174,DRB1*15:152 2 0 2 #> DRB1*04:56:02,DRB1*15:01:48 2 0 2 #> DRB1*14:172,DRB1*04:160 2 0 2 #> DRB1*04:359,DRB1*04:284:02 2 0 2 #> pos9_E pos9_W #> DRB1*12:02:02:03,DRB1*12:02:02:03,DRB1*14:54:02 3 0 #> DRB1*04:174,DRB1*15:152 1 1 #> DRB1*04:56:02,DRB1*15:01:48 1 1 #> DRB1*14:172,DRB1*04:160 2 0 #> DRB1*04:359,DRB1*04:284:02 2 0"},{"path":"https://slowkow.github.io/hlabud/reference/get_hlabud_dir.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","title":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","text":"function : Get folder name getOption(\"hlabud_dir\") else automatically choose appropriate folder operating system thanks rappdirs. Create folder automatically already exist. Set hlabud_dir option new folder.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/get_hlabud_dir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","text":"","code":"get_hlabud_dir()"},{"path":"https://slowkow.github.io/hlabud/reference/get_hlabud_dir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","text":"name folder.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/get_hlabud_dir.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","text":"locations hlabud_dir folder operating system. Linux: Mac: Windows: set hlabud_dir option, please use:","code":"~/.local/share/hlabud ~/Library/Application Support/hlabud C:\\Documents and Settings\\{User}\\Application Data\\slowkow\\hlabud options(hlabud_dir = \"/my/favorite/path\")"},{"path":"https://slowkow.github.io/hlabud/reference/get_hlabud_dir.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the name of the folder for caching downloaded IMGTHLA files — get_hlabud_dir","text":"","code":"if (FALSE) { hlabud_dir <- get_hlabud_dir() }"},{"path":"https://slowkow.github.io/hlabud/reference/get_onehot.html","id":null,"dir":"Reference","previous_headings":"","what":"Make a one-hot encoded matrix from a dataframe of amino acid\nsequences. — get_onehot","title":"Make a one-hot encoded matrix from a dataframe of amino acid\nsequences. — get_onehot","text":"Make one-hot encoded matrix dataframe amino acid sequences.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/get_onehot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make a one-hot encoded matrix from a dataframe of amino acid\nsequences. — get_onehot","text":"","code":"get_onehot(al, n_pre)"},{"path":"https://slowkow.github.io/hlabud/reference/get_onehot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make a one-hot encoded matrix from a dataframe of amino acid\nsequences. — get_onehot","text":"al dataframe columns allele, seq n_pre number amino acid sequences position 1.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_alignments.html","id":null,"dir":"Reference","previous_headings":"","what":"Get sequence alignments from IMGTHLA — hla_alignments","title":"Get sequence alignments from IMGTHLA — hla_alignments","text":"conventions used alignments (EBI IMGT-HLA help page): entry allele displayed respect reference sequences. identity reference sequence present base displayed hyphen (-). Non-identity reference sequence shown displaying appropriate base position. insertion deletion occurred represented period (.). sequence unknown point alignment, represented asterisk (*). protein alignments null alleles, 'Stop' codons represented hash (X). protein alignments, sequence following termination codon, marked appear blank. conventions used nucleotide protein alignments.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_alignments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get sequence alignments from IMGTHLA — hla_alignments","text":"","code":"hla_alignments( gene = \"DRB1\", type = \"prot\", release = \"latest\", verbose = FALSE )"},{"path":"https://slowkow.github.io/hlabud/reference/hla_alignments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get sequence alignments from IMGTHLA — hla_alignments","text":"gene name gene like \"DRB1\" type type sequence, one \"prot\", \"nuc\", \"gen\" release Default \"latest\". release name like \"3.51.0\". verbose TRUE, print messages along way.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_alignments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get sequence alignments from IMGTHLA — hla_alignments","text":"list dataframe called sequences two matrices alleles onehot. dataframe two columns: allele: name allele, e.g., DQB*01:01 seq: amino acid sequence matrix alleles one row allele, one column position, values representing residues position allele. matrix onehot one-hot encoding variants distinguish alleles, one row allele one column amino acid position.","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/hla_alignments.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get sequence alignments from IMGTHLA — hla_alignments","text":"","code":"# \\donttest{ a <- hla_alignments(\"DRB1\") head(a$sequences) #> # A tibble: 6 × 2 #> allele seq #> #> 1 DRB1*01:01:01:01 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVR.LLERC… #> 2 DRB1*01:01:01:02 ------------------------------------------------------.-----… #> 3 DRB1*01:01:01:03 ------------------------------------------------------.-----… #> 4 DRB1*01:01:01:04 ------------------------------------------------------.-----… #> 5 DRB1*01:01:01:05 ------------------------------------------------------.-----… #> 6 DRB1*01:01:01:06 ------------------------------------------------------.-----… a$alleles[1:6,1:6] #> posn29 posn28 posn27 posn26 posn25 posn24 #> DRB1*01:01:01:01 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" #> DRB1*01:01:01:02 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" #> DRB1*01:01:01:03 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" #> DRB1*01:01:01:04 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" #> DRB1*01:01:01:05 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" #> DRB1*01:01:01:06 \"M\" \"V\" \"C\" \"L\" \"K\" \"L\" a$onehot[1:6,1:6] #> posn29_unk posn29_M posn28_unk posn28_L posn28_V posn27_unk #> DRB1*01:01:01:01 0 1 0 0 1 0 #> DRB1*01:01:01:02 0 1 0 0 1 0 #> DRB1*01:01:01:03 0 1 0 0 1 0 #> DRB1*01:01:01:04 0 1 0 0 1 0 #> DRB1*01:01:01:05 0 1 0 0 1 0 #> DRB1*01:01:01:06 0 1 0 0 1 0 # }"},{"path":"https://slowkow.github.io/hlabud/reference/hla_alleles.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","title":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","text":"Download list allele names HLA genes particular IMGTHLA release.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_alleles.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","text":"","code":"hla_alleles(release = \"latest\", overwrite = FALSE, verbose = FALSE)"},{"path":"https://slowkow.github.io/hlabud/reference/hla_alleles.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","text":"release Default \"latest\". release name like \"3.51.0\". overwrite Overwrite existing alleles.json file Allelelist.{version}.txt file verbose TRUE, print messages along way.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_alleles.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","text":"data frame HLA allele ids names","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/hla_alleles.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get a table of allele names for a particular IMGTHLA release — hla_alleles","text":"","code":"# \\donttest{ head(hla_alleles()) #> AlleleID Allele #> 1 HLA00001 A*01:01:01:01 #> 2 HLA02169 A*01:01:01:02N #> 3 HLA14798 A*01:01:01:03 #> 4 HLA15760 A*01:01:01:04 #> 5 HLA16415 A*01:01:01:05 #> 6 HLA16417 A*01:01:01:06 # }"},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate HLA divergence for each individual — hla_divergence","title":"Calculate HLA divergence for each individual — hla_divergence","text":"First, convert allele name (e.g. *01:01) amino acid sequence. divergence sum distances pair amino acids position, divided total sequence length. amino acid distance matrix use one published Grantham 1974 (doi:10.1126/science.185.4154.862), based three physical properties amino acids (composition, polarity, molecular volume) correlated estimate relative substitution frequency.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate HLA divergence for each individual — hla_divergence","text":"","code":"hla_divergence( alleles = c(\"A*01:01,A*02:01\"), method = \"grantham\", release = \"latest\" )"},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate HLA divergence for each individual — hla_divergence","text":"alleles character vector comma-delimited alleles individual. usually expect two alleles per individual, possible (fewer) copies due copy number alterations. function still works individual different number alleles. method pairwise amino acid matrix, method name: \"grantham\" \"uniform\" indicate pairwise amino acid distance matrix use. choose pass matrix, 20x20 symmetric matrix zeros diagonal, rownames colnames one-letter amino acid codes R N D C Q E G H L K M F P S T W Y V. release Default \"latest\". release name like \"3.51.0\".","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate HLA divergence for each individual — hla_divergence","text":"dataframe divergence individual.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate HLA divergence for each individual — hla_divergence","text":"code function translation original Perl code Tobias Lenz, published Pierini & Lenz 2018 MolBiolEvol (https://doi.org/10.1093/molbev/msy116). comparing two amino acid sequences, characters one 20 amino acids considered divergence calculation, gaps (characters) count.","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/hla_divergence.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate HLA divergence for each individual — hla_divergence","text":"","code":"my_genos <- c(\"A*23:01:12,A*24:550\", \"A*25:12N,A*11:27\", \"A*24:381,A*33:85\", \"A*01:01:,A*01:01,A*02:01\") hla_divergence(my_genos, method = \"grantham\") #> A*23:01:12,A*24:550 A*25:12N,A*11:27 A*24:381,A*33:85 #> 0.4924242 3.3333333 4.9015152 #> A*01:01:,A*01:01,A*02:01 #> 3.8367003 # This is equivalent hla_divergence(my_genos, method = amino_distance_matrix(\"grantham\")) #> A*23:01:12,A*24:550 A*25:12N,A*11:27 A*24:381,A*33:85 #> 0.4924242 3.3333333 4.9015152 #> A*01:01:,A*01:01,A*02:01 #> 3.8367003"},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":null,"dir":"Reference","previous_headings":"","what":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"Download read table HLA allele frequencies Allele Frequency Net Database (AFND).","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"","code":"hla_frequencies(verbose = FALSE)"},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"verbose TRUE, print messages along way.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"dataframe HLA allele frequencies genes.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"use data, please cite latest manuscript Allele Frequency Net Database: Gonzalez-Galarza FF, McCabe , Santos EJMD, Jones J, Takeshita L, Ortega-Rivera ND, et al. Allele frequency net database (AFND) 2020 update: gold-standard data classification, open access genotype data new query tools. Nucleic Acids Res. 2020;48: D783–D788. doi:10.1093/nar/gkz1029","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_frequencies.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get HLA frequences from Allele Frequency Net Database (AFND) — hla_frequencies","text":"","code":"# \\donttest{ hla_frequencies() #> # A tibble: 123,502 × 7 #> group gene allele population indivs_over_n alleles_over_2n n #> #> 1 hla A A*01:01 Argentina Rosario To… 15.1 0.076 86 #> 2 hla A A*01:01 Armenia combined Reg… NA 0.125 100 #> 3 hla A A*01:01 Australia Cape York … NA 0.053 103 #> 4 hla A A*01:01 Australia Groote Eyl… NA 0.027 75 #> 5 hla A A*01:01 Australia New South … NA 0.187 134 #> 6 hla A A*01:01 Australia Yuendumu A… NA 0.008 191 #> 7 hla A A*01:01 Austria 27 0.146 200 #> 8 hla A A*01:01 Azores Central Islan… NA 0.08 59 #> 9 hla A A*01:01 Azores Oriental Isla… NA 0.115 43 #> 10 hla A A*01:01 Azores Terceira Isla… NA 0.109 130 #> # ℹ 123,492 more rows # }"},{"path":"https://slowkow.github.io/hlabud/reference/hla_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Get HLA gene names from IMGTHLA — hla_genes","title":"Get HLA gene names from IMGTHLA — hla_genes","text":"Retrieve list txt files github.com/ANHIG/IMGTHLA/alignments return list gene names derived file names.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get HLA gene names from IMGTHLA — hla_genes","text":"","code":"hla_genes(release = \"latest\", overwrite = FALSE, verbose = FALSE)"},{"path":"https://slowkow.github.io/hlabud/reference/hla_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get HLA gene names from IMGTHLA — hla_genes","text":"release Default \"latest\". release name like \"3.51.0\". overwrite Overwrite existing genes.json file new one GitHub verbose TRUE, print messages along way.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get HLA gene names from IMGTHLA — hla_genes","text":"tibble two columns: HLA gene names (\"\", \"DRB1\") types (\"nuc\", \"gen\", \"prot\").","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/hla_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get HLA gene names from IMGTHLA — hla_genes","text":"","code":"# \\donttest{ hla_genes() #> # A tibble: 107 × 2 #> gene type #> #> 1 A gen #> 2 A nuc #> 3 A prot #> 4 B gen #> 5 B nuc #> 6 B prot #> 7 C gen #> 8 C nuc #> 9 C prot #> 10 DMA gen #> # ℹ 97 more rows # }"},{"path":"https://slowkow.github.io/hlabud/reference/hla_releases.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the names of releases from IMGTHLA — hla_releases","title":"Get the names of releases from IMGTHLA — hla_releases","text":"Get tags github.com/ANHIG/IMGTHLA, save file called tags.json getOption(\"hlabud_dir\"), return release names file.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_releases.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the names of releases from IMGTHLA — hla_releases","text":"","code":"hla_releases(overwrite = FALSE)"},{"path":"https://slowkow.github.io/hlabud/reference/hla_releases.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the names of releases from IMGTHLA — hla_releases","text":"overwrite Overwrite existing tags.json file getOption(\"hlabud_dir\")","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_releases.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the names of releases from IMGTHLA — hla_releases","text":"character vector release names like \"3.51.0\"","code":""},{"path":"https://slowkow.github.io/hlabud/reference/hla_releases.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the names of releases from IMGTHLA — hla_releases","text":"","code":"# \\donttest{ hla_releases() #> [1] \".354.0\" \"3.53.0\" \"3.52.0\" \"3.51.0\" \"3.50.0\" \"3.49.0\" #> [7] \"3.48.0\" \"3.47.0\" \"3.46.0\" \"3.45.1\" \"3.45.01\" \"3.45.0.1\" #> [13] \"3.45.0\" \"3.44.1\" \"3.44.0\" \"3.43.0\" \"3.42.0\" \"3.41.2\" #> [19] \"3.41.0\" \"3.40.0\" \"3.39.0\" \"3.38.0\" \"3.37.0\" \"3.36.0\" #> [25] \"3.35.0\" \"3.34.0\" \"3.33.0\" \"3.32.0\" \"3.31.0\" \"3.30.0\" # }"},{"path":"https://slowkow.github.io/hlabud/reference/hlabud-package.html","id":null,"dir":"Reference","previous_headings":"","what":"hlabud: Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA — hlabud-package","title":"hlabud: Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA — hlabud-package","text":"Fetch sequence alignment data IMGTHLA database Robinson et al (2020) doi:10.1093/nar/gkz950 , automatically convert sequence alignments convenient R matrices ready downstream analysis. vignette shows examples using one-hot encoding data logistic regression dimensionality reduction. Data downloaded lazily, -needed, cached user-configurable folder.","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/hlabud-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"hlabud: Methods for Access and Analysis of the Human Leukocyte Antigen (HLA) Gene Sequence Alignments from IMGTHLA — hlabud-package","text":"Maintainer: Kamil Slowikowski kslowikowski@gmail.com (ORCID)","code":""},{"path":"https://slowkow.github.io/hlabud/reference/install_hla.html","id":null,"dir":"Reference","previous_headings":"","what":"Download and unpack a tarball release from IMGTHLA — install_hla","title":"Download and unpack a tarball release from IMGTHLA — install_hla","text":"release tarball Github unpacked getOption(\"hlabud_dir\") folder.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/install_hla.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Download and unpack a tarball release from IMGTHLA — install_hla","text":"","code":"install_hla(release = \"latest\", overwrite = FALSE, verbose = FALSE)"},{"path":"https://slowkow.github.io/hlabud/reference/install_hla.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Download and unpack a tarball release from IMGTHLA — install_hla","text":"release Default \"latest\". release name like \"3.51.0\". overwrite TRUE, overwrite existing files release folder. verbose TRUE, print messages along way.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/install_hla.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Download and unpack a tarball release from IMGTHLA — install_hla","text":"Note latest releases 100 MB size, download might take slow connections.","code":""},{"path":[]},{"path":"https://slowkow.github.io/hlabud/reference/install_hla.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Download and unpack a tarball release from IMGTHLA — install_hla","text":"","code":"if (FALSE) { install_hla() install_hla(\"3.51.0\") install_hla(\"3.51.0\", verbose = TRUE) # Change the install directory options(hlabud_dir = \"path/to/my/dir\") install_hla() }"},{"path":"https://slowkow.github.io/hlabud/reference/one_to_three.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert one letter amino acid codes to three letter amino acid codes — one_to_three","title":"Convert one letter amino acid codes to three letter amino acid codes — one_to_three","text":"Convert one letter amino acid codes three letter amino acid codes","code":""},{"path":"https://slowkow.github.io/hlabud/reference/one_to_three.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert one letter amino acid codes to three letter amino acid codes — one_to_three","text":"","code":"one_to_three(aminos)"},{"path":"https://slowkow.github.io/hlabud/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling rhs(lhs).","code":""},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":null,"dir":"Reference","previous_headings":"","what":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"function reads txt files provided IMGTHLA.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"","code":"read_alignments(file)"},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"file File name txt file IMGTHLA like \"DQB1_prot.txt\"","code":""},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"list dataframe called sequences two matrices alleles onehot. dataframe two columns: allele: name allele, e.g., DQB*01:01 seq: amino acid sequence matrix alleles one row allele, one column position, values representing residues position allele. matrix onehot one-hot encoding variants distinguish alleles, one row allele one column amino acid position.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"Consider using hla_alignments() instead function. already txt file want read, can read read_alignments(\"myfile.txt\"). sequences contained file: {gene}_prot.txt amino acid sequence HLA allele. {gene}_nuc.txt nucleotide sequence exons. {gene}_gen.txt genomic sequence exons introns.","code":""},{"path":"https://slowkow.github.io/hlabud/reference/read_alignments.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read an alignment file *_(nuc|gen|prot).txt from IMGTHLA — read_alignments","text":"","code":"my_file <- file.path( \"https://github.com/ANHIG/IMGTHLA/raw\", \"5f2c562056f8ffa89aeea0631f2a52300ee0de17\", \"alignments/DRB1_prot.txt\" ) a <- read_alignments(my_file) head(a$sequences) #> # A tibble: 6 × 2 #> allele seq #> #> 1 DRB1*01:01:01:01 MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVR.LLERC… #> 2 DRB1*01:01:01:02 ------------------------------------------------------.-----… #> 3 DRB1*01:01:01:03 ------------------------------------------------------.-----… #> 4 DRB1*01:01:01:04 ------------------------------------------------------.-----… #> 5 DRB1*01:01:01:05 ------------------------------------------------------.-----… #> 6 DRB1*01:01:01:06 ------------------------------------------------------.-----… a$alleles[1:5,1:5] #> posn29 posn28 posn27 posn26 posn25 #> DRB1*01:01:01:01 \"M\" \"V\" \"C\" \"L\" \"K\" #> DRB1*01:01:01:02 \"M\" \"V\" \"C\" \"L\" \"K\" #> DRB1*01:01:01:03 \"M\" \"V\" \"C\" \"L\" \"K\" #> DRB1*01:01:01:04 \"M\" \"V\" \"C\" \"L\" \"K\" #> DRB1*01:01:01:05 \"M\" \"V\" \"C\" \"L\" \"K\" a$onehot[1:5,1:5] #> posn29_unk posn29_M posn28_unk posn28_V posn27_unk #> DRB1*01:01:01:01 0 1 0 1 0 #> DRB1*01:01:01:02 0 1 0 1 0 #> DRB1*01:01:01:03 0 1 0 1 0 #> DRB1*01:01:01:04 0 1 0 1 0 #> DRB1*01:01:01:05 0 1 0 1 0"},{"path":"https://slowkow.github.io/hlabud/news/index.html","id":"hlabud-1009999","dir":"Changelog","previous_headings":"","what":"hlabud 1.0.0.9999","title":"hlabud 1.0.0.9999","text":"Instead discarding positions *, include label unk, example pos241_unk indicates unknown amino acid position 241. Thanks Sreekar Mantena reporting issue! Fix --one error. example, HLA-pos361_- colnames($onehot) reference allele instead -. now fixed. Thanks Sreekar Mantena reporting issue!","code":""},{"path":"https://slowkow.github.io/hlabud/news/index.html","id":"hlabud-100","dir":"Changelog","previous_headings":"","what":"hlabud 1.0.0","title":"hlabud 1.0.0","text":"Added NEWS.md file track changes package.","code":""}]