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Hi Dr. Gosselin,
I used the radiator package to read in my vcf
vcf <- read_vcf(data = "populations.snps.vcf", strata = "Whitefish.strata.tsv", parallel.core = 1L)
I then attempted to use the grur package to perform the identity by missingness analysis and got an error.
ibm.whitefish<-missing_visualization(
vcf,
strata = "Whitefish.strata.tsv",
distance.method = "euclidean",
ind.missing.geno.threshold = c(2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90),
filename = NULL,
parallel.core = 1L,
write.plot = TRUE
)
Here is the output
Default "..." arguments assigned in missing_visualization:
path.folder = NULL
Number of duplicate id: 0
Number of chrom/scaffolds: 1
Number of locus: 182
Number of SNPs: 350
Proportion of missing genotypes (overall): 0.144619
Identity-by-missingness (IBM) analysis using
Principal Coordinate Analysis (PCoA)...
fstcore package v0.9.12
(OpenMP detected, using 12 threads)
Generating Identity by missingness plot
Redundancy analysis... Error in eigen(delta1) : infinite or missing values in 'x'
In addition: Warning message:
package ‘fstcore’ was built under R version 4.1.3
Computation time, overall: 5 sec
I saw in another error report that someone got the same error when attempting missing_visualization on a genlight object and you suggested it was because one of the pop groups had a size of 1 but that is not the case here. I have 33 populations (strata) and the smallest size is 5.
Here are the results from running session_info()
devtools::session_info()
Session info ----------------------------------------------------------------------------------------
setting value
version R version 4.1.0 (2021-05-18)
os Windows 10 x64 (build 19044)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz America/Denver
date 2022-07-13
rstudio 2022.02.3+492 Prairie Trillium (desktop)
pandoc NA
Hi Dr. Gosselin,
I used the radiator package to read in my vcf
vcf <- read_vcf(data = "populations.snps.vcf", strata = "Whitefish.strata.tsv", parallel.core = 1L)
I then attempted to use the grur package to perform the identity by missingness analysis and got an error.
ibm.whitefish<-missing_visualization(
vcf,
strata = "Whitefish.strata.tsv",
distance.method = "euclidean",
ind.missing.geno.threshold = c(2, 5, 10, 20, 30, 40, 50, 60, 70, 80, 90),
filename = NULL,
parallel.core = 1L,
write.plot = TRUE
)
Here is the output
Default "..." arguments assigned in missing_visualization:
path.folder = NULL
Folder created: missing_visualization_20220713@1009
File written: [email protected]
Importing data
File written: individuals qc info and stats summary
File written: individuals qc plot
Informations:
Number of populations: 33
Number of individuals: 545
Number of ind/pop:
CclPEND21C = 15
PabBERL20C = 16
PgeBERL19C = 32
PspBERL20C = 16
PwiBGLR2021C = 26
PwiBHNR20C = 14
PwiBIGW0321C = 47
PwiBOIS20C = 18
PwiBRUN21C = 15
PwiCLFR21C = 16
PwiCLWR20C = 16
PwiEFSW14C = 16
PwiGALL20C = 16
PwiHFRK21C = 15
PwiKOTN21C = 14
PwiKOTN21C_1 = 15
PwiLKGC20C = 15
PwiLOGN20C = 16
PwiLSTW20C = 16
PwiMDSN20C = 16
PwiMFWR20C = 16
PwiNFBR21C = 12
PwiNFSR21C = 16
PwiRFLC20C = 16
PwiSFBR21C = 5
PwiSFSN20C = 15
PwiSQPR20C = 11
PwiSTMP20C = 16
PwiTETR20C = 16
PwiTRUC09C = 13
PwiWBSL20C = 16
PwiWLWL20C = 15
PwoYLOR21C = 8
Number of duplicate id: 0
Number of chrom/scaffolds: 1
Number of locus: 182
Number of SNPs: 350
Proportion of missing genotypes (overall): 0.144619
Identity-by-missingness (IBM) analysis using
Principal Coordinate Analysis (PCoA)...
fstcore package v0.9.12
(OpenMP detected, using 12 threads)
Generating Identity by missingness plot
Redundancy analysis...
Error in eigen(delta1) : infinite or missing values in 'x'
In addition: Warning message:
package ‘fstcore’ was built under R version 4.1.3
Computation time, overall: 5 sec
I saw in another error report that someone got the same error when attempting missing_visualization on a genlight object and you suggested it was because one of the pop groups had a size of 1 but that is not the case here. I have 33 populations (strata) and the smallest size is 5.
Here are the results from running session_info()
devtools::session_info()
Session info ----------------------------------------------------------------------------------------
setting value
version R version 4.1.0 (2021-05-18)
os Windows 10 x64 (build 19044)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_United States.1252
ctype English_United States.1252
tz America/Denver
date 2022-07-13
rstudio 2022.02.3+492 Prairie Trillium (desktop)
pandoc NA
Packages --------------------------------------------------------------------------------------------
package * version date (UTC) lib source
abind 1.4-5 2016-07-21 [1] CRAN (R 4.1.0)
ade4 1.7-19 2022-04-19 [1] CRAN (R 4.1.3)
adegenet 2.1.7 2022-06-06 [1] CRAN (R 4.1.3)
adegraphics 1.0-16 2021-09-16 [1] CRAN (R 4.1.3)
adephylo 1.1-11 2017-12-18 [1] CRAN (R 4.1.3)
adespatial 0.3-16 2022-03-31 [1] CRAN (R 4.1.3)
ape 5.6-2 2022-03-02 [1] CRAN (R 4.1.3)
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.1.1)
backports 1.4.1 2021-12-13 [1] CRAN (R 4.1.2)
BiocGenerics 0.40.0 2021-10-26 [1] Bioconductor
Biostrings 2.62.0 2021-10-26 [1] Bioconductor
bit 4.0.4 2020-08-04 [1] CRAN (R 4.1.2)
bit64 4.0.5 2020-08-30 [1] CRAN (R 4.1.2)
bitops 1.0-7 2021-04-24 [1] CRAN (R 4.1.1)
boot 1.3-28 2021-05-03 [2] CRAN (R 4.1.0)
broom 1.0.0 2022-07-01 [1] CRAN (R 4.1.3)
cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.2)
callr 3.7.1 2022-07-13 [1] CRAN (R 4.1.0)
car 3.1-0 2022-06-15 [1] CRAN (R 4.1.3)
carData 3.0-5 2022-01-06 [1] CRAN (R 4.1.2)
class 7.3-19 2021-05-03 [2] CRAN (R 4.1.0)
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cli 3.3.0 2022-04-25 [1] CRAN (R 4.1.3)
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codetools 0.2-18 2020-11-04 [2] CRAN (R 4.1.0)
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data.table 1.14.2 2021-09-27 [1] CRAN (R 4.1.2)
DBI 1.1.3 2022-06-18 [1] CRAN (R 4.1.3)
deldir 1.0-6 2021-10-23 [1] CRAN (R 4.1.1)
devtools 2.4.3 2021-11-30 [1] CRAN (R 4.1.2)
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e1071 1.7-11 2022-06-07 [1] CRAN (R 4.1.3)
EFGLmh 0.1.0 2021-06-14 [1] Github (delomast/EFGLmh@dbb9612)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
fansi 1.0.3 2022-03-24 [1] CRAN (R 4.1.3)
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fs 1.5.2 2021-12-08 [1] CRAN (R 4.1.2)
fst 0.9.8 2022-02-08 [1] CRAN (R 4.1.3)
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gdsfmt 1.30.0 2021-10-26 [1] Bioconductor
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GenomeInfoDb 1.30.1 2022-01-30 [1] Bioconductor
GenomeInfoDbData 1.2.7 2022-02-14 [1] Bioconductor
GenomicRanges 1.46.1 2021-11-18 [1] Bioconductor
ggplot2 3.3.6 2022-05-03 [1] CRAN (R 4.1.3)
ggpubr 0.4.0 2020-06-27 [1] CRAN (R 4.1.0)
ggsignif 0.6.3 2021-09-09 [1] CRAN (R 4.1.2)
glue 1.6.2 2022-02-24 [1] CRAN (R 4.1.3)
gridExtra 2.3 2017-09-09 [1] CRAN (R 4.1.2)
grur * 0.1.4 2022-07-12 [1] Github (d31c423)
gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.0)
hms 1.1.1 2021-09-26 [1] CRAN (R 4.1.2)
htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.2)
httpuv 1.6.5 2022-01-05 [1] CRAN (R 4.1.2)
httr 1.4.3 2022-05-04 [1] CRAN (R 4.1.3)
igraph 1.3.2 2022-06-13 [1] CRAN (R 4.1.3)
interp 1.1-2 2022-05-10 [1] CRAN (R 4.1.3)
IRanges 2.28.0 2021-10-26 [1] Bioconductor
jpeg 0.1-9 2021-07-24 [1] CRAN (R 4.1.1)
KernSmooth 2.23-20 2021-05-03 [2] CRAN (R 4.1.0)
labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.0)
later 1.3.0 2021-08-18 [1] CRAN (R 4.1.2)
lattice 0.20-44 2021-05-02 [2] CRAN (R 4.1.0)
latticeExtra 0.6-30 2022-07-04 [1] CRAN (R 4.1.3)
lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.3)
lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.1.2)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.1.3)
MASS 7.3-54 2021-05-03 [2] CRAN (R 4.1.0)
Matrix 1.3-3 2021-05-04 [2] CRAN (R 4.1.0)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.1.2)
mgcv 1.8-35 2021-04-18 [2] CRAN (R 4.1.0)
mime 0.12 2021-09-28 [1] CRAN (R 4.1.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.0)
nlme 3.1-152 2021-02-04 [2] CRAN (R 4.1.0)
permute 0.9-7 2022-01-27 [1] CRAN (R 4.1.2)
phylobase 0.8.10 2020-03-01 [1] CRAN (R 4.1.3)
pillar 1.7.0 2022-02-01 [1] CRAN (R 4.1.2)
pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.1.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.0)
pkgload 1.3.0 2022-06-27 [1] CRAN (R 4.1.3)
plyr 1.8.7 2022-03-24 [1] CRAN (R 4.1.3)
png 0.1-7 2013-12-03 [1] CRAN (R 4.1.1)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.0)
processx 3.7.0 2022-07-07 [1] CRAN (R 4.1.3)
progress 1.2.2 2019-05-16 [1] CRAN (R 4.1.0)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.1.0)
proxy 0.4-27 2022-06-09 [1] CRAN (R 4.1.3)
ps 1.7.1 2022-06-18 [1] CRAN (R 4.1.3)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.0)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.2)
radiator * 1.2.2 2022-07-12 [1] Github (thierrygosselin/radiator@6efdf14)
raster 3.5-21 2022-06-27 [1] CRAN (R 4.1.3)
RColorBrewer 1.1-3 2022-04-03 [1] CRAN (R 4.1.3)
Rcpp 1.0.8.3 2022-03-17 [1] CRAN (R 4.1.3)
RCurl 1.98-1.7 2022-06-09 [1] CRAN (R 4.1.3)
readr 2.1.2 2022-01-30 [1] CRAN (R 4.1.2)
remotes 2.4.2 2021-11-30 [1] CRAN (R 4.1.2)
reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.2)
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rncl 0.8.6 2022-03-18 [1] CRAN (R 4.1.3)
RNeXML 2.4.7 2022-05-13 [1] CRAN (R 4.1.3)
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rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.1)
s2 1.0.7 2021-09-28 [1] CRAN (R 4.1.2)
S4Vectors 0.32.4 2022-04-03 [1] Bioconductor
scales 1.2.0 2022-04-13 [1] CRAN (R 4.1.3)
SeqArray 1.34.0 2021-10-26 [1] Bioconductor
seqinr 4.2-16 2022-05-19 [1] CRAN (R 4.1.3)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.1.2)
sf 1.0-7 2022-03-07 [1] CRAN (R 4.1.3)
shiny 1.7.1 2021-10-02 [1] CRAN (R 4.1.2)
sp 1.5-0 2022-06-05 [1] CRAN (R 4.1.3)
spData 2.0.1 2021-10-14 [1] CRAN (R 4.1.2)
spdep 1.2-4 2022-04-18 [1] CRAN (R 4.1.3)
stringi 1.7.6 2021-11-29 [1] CRAN (R 4.1.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.0)
terra 1.5-34 2022-06-09 [1] CRAN (R 4.1.3)
tibble 3.1.7 2022-05-03 [1] CRAN (R 4.1.3)
tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.1.3)
tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.1.3)
tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.1.3)
units 0.8-0 2022-02-05 [1] CRAN (R 4.1.2)
UpSetR 1.4.0 2019-05-22 [1] CRAN (R 4.1.3)
usethis 2.1.6 2022-05-25 [1] CRAN (R 4.1.3)
utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.3)
uuid 1.1-0 2022-04-19 [1] CRAN (R 4.1.3)
vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.1.3)
vegan 2.6-2 2022-04-17 [1] CRAN (R 4.1.3)
vroom 1.5.7 2021-11-30 [1] CRAN (R 4.1.2)
withr 2.5.0 2022-03-03 [1] CRAN (R 4.1.3)
wk 0.6.0 2022-01-03 [1] CRAN (R 4.1.2)
XML 3.99-0.10 2022-06-09 [1] CRAN (R 4.1.3)
xml2 1.3.3 2021-11-30 [1] CRAN (R 4.1.2)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.1.0)
XVector 0.34.0 2021-10-26 [1] Bioconductor
zlibbioc 1.40.0 2021-10-26 [1] Bioconductor
I've attached my strata file and the first 100 lines of my vcf file as txt files
trunc.populations.snps.vcf.txt
Whitefish.strata.tsv.txt
Thanks for any help,
Kat
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