From 46f5ffadc9b4848a47df3b53ad88e42e5cd5aa2d Mon Sep 17 00:00:00 2001 From: yixuan-chen-elisa Date: Mon, 20 Nov 2023 00:52:11 -0500 Subject: [PATCH] update test data & news --- R/read.modbam2bed.R | 61 ++++---- R/read.modkit.R | 134 +++++++++--------- inst/NEWS.Rd | 9 +- inst/extdata/modbam2bed/Ctr1.bed.gz | Bin 15430 -> 0 bytes inst/extdata/modbam2bed/Ctr2.bed.gz | Bin 15536 -> 0 bytes inst/extdata/modbam2bed/Ctr3.bed.gz | Bin 15364 -> 0 bytes inst/extdata/modbam2bed/Tret1.bed.gz | Bin 15768 -> 0 bytes inst/extdata/modbam2bed/Tret2.bed.gz | Bin 15601 -> 0 bytes inst/extdata/modbam2bed/Tret3.bed.gz | Bin 15989 -> 0 bytes .../modbam2bed/ctr1.chr10.chr11.bed.gz | Bin 0 -> 17109 bytes .../modbam2bed/ctr2.chr10.chr11.bed.gz | Bin 0 -> 17121 bytes .../modbam2bed/ctr3.chr10.chr11.bed.gz | Bin 0 -> 16908 bytes .../modbam2bed/tret1.chr10.chr11.bed.gz | Bin 0 -> 17077 bytes .../modbam2bed/tret2.chr10.chr11.bed.gz | Bin 0 -> 17196 bytes .../modbam2bed/tret3.chr10.chr11.bed.gz | Bin 0 -> 16948 bytes man/read.modbam2bed.Rd | 44 +++--- man/read.modkit.Rd | 20 +-- tests/testthat/test_read.modbam2bed.R | 2 +- 18 files changed, 139 insertions(+), 131 deletions(-) delete mode 100644 inst/extdata/modbam2bed/Ctr1.bed.gz delete mode 100644 inst/extdata/modbam2bed/Ctr2.bed.gz delete mode 100644 inst/extdata/modbam2bed/Ctr3.bed.gz delete mode 100644 inst/extdata/modbam2bed/Tret1.bed.gz delete mode 100644 inst/extdata/modbam2bed/Tret2.bed.gz delete mode 100644 inst/extdata/modbam2bed/Tret3.bed.gz create mode 100644 inst/extdata/modbam2bed/ctr1.chr10.chr11.bed.gz create mode 100644 inst/extdata/modbam2bed/ctr2.chr10.chr11.bed.gz create mode 100644 inst/extdata/modbam2bed/ctr3.chr10.chr11.bed.gz create mode 100644 inst/extdata/modbam2bed/tret1.chr10.chr11.bed.gz create mode 100644 inst/extdata/modbam2bed/tret2.chr10.chr11.bed.gz create mode 100644 inst/extdata/modbam2bed/tret3.chr10.chr11.bed.gz diff --git a/R/read.modbam2bed.R b/R/read.modbam2bed.R index 6792854..2317135 100644 --- a/R/read.modbam2bed.R +++ b/R/read.modbam2bed.R @@ -1,35 +1,35 @@ read.modbam2bed <- function(files, colData = NULL, rmZeroCov = FALSE, strandCollapse = TRUE) { - gr_list <- list() - sampleNames <- sub("\\.bed$","",basename(files)) - if (!is.null(colData)) { - rownames(colData) <- sampleNames - } + gr_list <- list() + sampleNames <- sub("\\.bed$","",basename(files)) + if (!is.null(colData)) { + rownames(colData) <- sampleNames + } - for (i in seq_along(files)) { - data <- read.table(files[i],header = FALSE, sep="\t", - stringsAsFactors=FALSE, quote="") - gr <- GRanges(seqnames = data$V1, - ranges = IRanges(start = data$V2+1, end = data$V3)) - mcols(gr)$m <- data$V13 - mcols(gr)$cov <- data$V12 + data$V13 - mcols(gr)$filter <- data$V14 - names(gr) <- sampleNames[i] - gr_list[[sampleNames[i]]] <- gr - } + for (i in seq_along(files)) { + data <- read.table(files[i],header = FALSE, sep="\t", + stringsAsFactors=FALSE, quote="") + gr <- GRanges(seqnames = data$V1, + ranges = IRanges(start = data$V2+1, end = data$V3)) + mcols(gr)$m <- data$V13 + mcols(gr)$cov <- data$V12 + data$V13 + mcols(gr)$filter <- data$V14 + names(gr) <- sampleNames[i] + gr_list[[sampleNames[i]]] <- gr + } - overlap_gr <- Reduce(subsetByOverlaps, gr_list) - - m_cov_list <- lapply(gr_list, function(gr) { - overlap_data = gr[gr %over% overlap_gr] - data.frame(m = overlap_data$m, cov = overlap_data$cov, - filter = overlap_data$filter)}) + overlap_gr <- Reduce(subsetByOverlaps, gr_list) - m <- do.call(cbind,lapply(m_cov_list,`[[`, "m")) - cov <- do.call(cbind, lapply(m_cov_list, `[[`, "cov")) - filter <- do.call(cbind, lapply(m_cov_list, `[[`, "filter")) + m_cov_list <- lapply(gr_list, function(gr) { + overlap_data <- gr[gr %over% overlap_gr] + data.frame(m = overlap_data$m, cov = overlap_data$cov, + filter = overlap_data$filter)}) - bsseq_obj <- BSseq(M = as.matrix(m), Cov = as.matrix(cov), + m <- do.call(cbind,lapply(m_cov_list,`[[`, "m")) + cov <- do.call(cbind, lapply(m_cov_list, `[[`, "cov")) + filter <- do.call(cbind, lapply(m_cov_list, `[[`, "filter")) + + bsseq_obj <- BSseq(M = as.matrix(m), Cov = as.matrix(cov), Filtered = as.matrix(filter), coef = NULL,se.coef = NULL, pos = start(overlap_gr),trans = NULL, @@ -37,8 +37,9 @@ read.modbam2bed <- function(files, colData = NULL, rmZeroCov = FALSE, chr = as.vector(seqnames(overlap_gr)), sampleNames = sampleNames,rmZeroCov = rmZeroCov) - if (strandCollapse) { - strandCollapse(bsseq_obj) - } - return(bsseq_obj) + if (strandCollapse) { + strandCollapse(bsseq_obj) + } + + return(bsseq_obj) } diff --git a/R/read.modkit.R b/R/read.modkit.R index d5f19ff..6a3f46e 100644 --- a/R/read.modkit.R +++ b/R/read.modkit.R @@ -1,78 +1,78 @@ -read.modkit = function(files, - colData = NULL, - rmZeroCov = FALSE, - strandCollapse = TRUE){ - gr_list = list() - sampleNames = sub("\\.bed$", "", basename(files)) - if (!is.null(colData)){ - rownames(colData) <- sampleNames - } +read.modkit <- function(files, + colData = NULL, + rmZeroCov = FALSE, + strandCollapse = TRUE){ + gr_list <- list() + sampleNames <- sub("\\.bed$", "", basename(files)) + if (!is.null(colData)){ + rownames(colData) <- sampleNames + } - for (i in seq_along(files)){ - data = read.table(files[i], header = FALSE, sep="\t", - stringsAsFactors=FALSE, quote="") + for (i in seq_along(files)){ + data <- read.table(files[i], header = FALSE, sep="\t", + stringsAsFactors=FALSE, quote="") + gr <- GRanges(seqnames = data$V1, + ranges = IRanges(start = data$V2+1, end = data$V3)) + mcols(gr)$m <- data$V12 + mcols(gr)$cov <- data$V12 + data$V13 + mcols(gr)$filter <- data$V16 + if (any(data$V14 != 0)){ + mcols(gr)$other_mod <- data$V14 + mcols(gr)$cov_other_mod <- data$V14 + data$V13 + } + names(gr) <- sampleNames[i] + gr_list[[sampleNames[i]]] <- gr + } - gr = GRanges(seqnames = data$V1, - ranges = IRanges(start = data$V2+1, end = data$V3)) - mcols(gr)$m = data$V12 - mcols(gr)$cov = data$V12 + data$V13 - mcols(gr)$filter = data$V16 - if (any(data$V14 != 0)){ - mcols(gr)$other_mod = data$V14 - mcols(gr)$cov_other_mod = data$V14 + data$V13} - names(gr) = sampleNames[i] - gr_list[[sampleNames[i]]] = gr - } + overlap_gr <- Reduce(subsetByOverlaps, gr_list) - overlap_gr = Reduce(subsetByOverlaps, gr_list) + m_cov_list <- lapply(gr_list, function(gr){ + overlap_data <- gr[gr %over% overlap_gr] + if (!is.null(gr$other_mod)) { + data.frame(m = overlap_data$m, cov = overlap_data$cov, + filter = overlap_data$filter, + other_mod = overlap_data$other_mod, + cov_other_mod = overlap_data$cov_other_mod) + } else { + data.frame(m = overlap_data$m, cov = overlap_data$cov, + filter = overlap_data$filter) + } + }) - m_cov_list = lapply(gr_list, function(gr){ - overlap_data = gr[gr %over% overlap_gr] - if (!is.null(gr$other_mod)) { - data.frame(m = overlap_data$m, cov = overlap_data$cov, - filter = overlap_data$filter, - other_mod = overlap_data$other_mod, - cov_other_mod = overlap_data$cov_other_mod) - } else { - data.frame(m = overlap_data$m, cov = overlap_data$cov, - filter = overlap_data$filter) - } - }) + m <- do.call(cbind, lapply(m_cov_list, `[[`, "m")) + cov <- do.call(cbind, lapply(m_cov_list, `[[`, "cov")) + filter <- do.call(cbind, lapply(m_cov_list, `[[`, "filter")) + other_mod <- do.call(cbind, lapply(m_cov_list, `[[`, "other_mod")) + cov_other_mod <- do.call(cbind, lapply(m_cov_list, `[[`, "cov_other_mod")) - m = do.call(cbind, lapply(m_cov_list, `[[`, "m")) - cov = do.call(cbind, lapply(m_cov_list, `[[`, "cov")) - filter = do.call(cbind, lapply(m_cov_list, `[[`, "filter")) - other_mod = do.call(cbind, lapply(m_cov_list, `[[`, "other_mod")) - cov_other_mod = do.call(cbind, lapply(m_cov_list, `[[`, "cov_other_mod")) + bsseq_objs <- list() + bsseq_obj_m <- BSseq(M = as.matrix(m), Cov = as.matrix(cov), + Filtered = as.matrix(filter), + coef = NULL, se.coef = NULL, + pos = start(overlap_gr), trans = NULL, + parameters = NULL, pData = colData, gr = NULL, + chr = as.vector(seqnames(overlap_gr)), + sampleNames = sampleNames, rmZeroCov = rmZeroCov) - bsseq_objs = list() - bsseq_obj_m = BSseq(M = as.matrix(m), Cov = as.matrix(cov), - Filtered = as.matrix(filter), - coef = NULL, se.coef = NULL, - pos = start(overlap_gr), trans = NULL, - parameters = NULL, pData = colData, gr = NULL, - chr = as.vector(seqnames(overlap_gr)), - sampleNames = sampleNames, rmZeroCov = rmZeroCov) + bsseq_objs[[1]] <- bsseq_obj_m - bsseq_objs[[1]] = bsseq_obj_m + if (!is.null(other_mod)){ + bsseq_obj_other_mod <- BSseq(M = as.matrix(other_mod), + Cov = as.matrix(cov_other_mod), + Filtered = as.matrix(filter), + coef = NULL, se.coef = NULL, + pos = start(overlap_gr), trans = NULL, + parameters = NULL, pData = colData, gr = NULL, + chr = as.vector(seqnames(overlap_gr)), + sampleNames = sampleNames, rmZeroCov = rmZeroCov) - if (!is.null(other_mod)){ - bsseq_obj_other_mod = BSseq(M = as.matrix(other_mod), - Cov = as.matrix(cov_other_mod), - Filtered = as.matrix(filter), - coef = NULL, se.coef = NULL, - pos = start(overlap_gr), trans = NULL, - parameters = NULL, pData = colData, gr = NULL, - chr = as.vector(seqnames(overlap_gr)), - sampleNames = sampleNames, rmZeroCov = rmZeroCov) + bsseq_objs[[2]] <- bsseq_obj_other_mod + } - bsseq_objs[[2]] = bsseq_obj_other_mod - } + if (strandCollapse){ + for (i in seq_along(bsseq_objs)) { + bsseq:::strandCollapse(bsseq_objs[[i]])} + } - if (strandCollapse){ - for (i in 1:length(bsseq_objs)) { - bsseq:::strandCollapse(bsseq_objs[[i]])} - } - - return(bsseq_objs) + return(bsseq_objs) } diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd index fc39bb0..ddba61f 100644 --- a/inst/NEWS.Rd +++ b/inst/NEWS.Rd @@ -8,9 +8,16 @@ years. } \item{Minor code and documentation chnages. Fixed usage of \code{class(x) == "y"} and added examples to some man pages.} + \item{\code{Bsseq()} is modified to store filtered matrix (ambigious modification status) for nanopore data. + } + \item{New function \code{read.modkit()} to read in methyl bed files generated from modkit and construct Bsseq objects. When there is no other modifications, one Bsseq object is constructed, and when there is other modification present, its methylation and corresponding coverage are also stored + and two Bsseq objects are constructed. + } + \item{New function \code{read.modbam2bed()} to read in, extract methylation, coverage and filtered data and create Bsseq object from methyl bed files obtained by modbam2bed. Some instructions for using modbam2bed is also provided. + } } } - + \section{Version 1.17.x}{ \itemize{ diff --git a/inst/extdata/modbam2bed/Ctr1.bed.gz b/inst/extdata/modbam2bed/Ctr1.bed.gz deleted file mode 100644 index c3fea0b8cc99b337be7fdca92f017871b5a72057..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 15430 zcmX9_bzGC*+ZK@$kX9OL7(GB72uLGcqZ>9lq`q`_isa~!F6ok%9!L)mP*4Vp1_=@H zef+)u?X%C5=Q-!Puec9W0zN)Jk_h$yTh7Zvh~FA!`yi=Db&kDij_u{WKOdh`o>*c4 z_umg3qE&Y!v;hyw(YC(ppIB%SD!ZFWR@B#jZyWwn6!cLR?8M0k-DUi}`+GOb^fy=l z^E+fmI>hQe=0^3R;cmNc=kM>rI&#e5E|j+nblOm1p%U`892=1xvBe{txe7l279x!E zm&VIj4=KPP7lirw=>*EF>XJVQ_P)1)s+eBuG%o1VY#MyEC|boud^+K?scaCh=LYp+ zMs!R#JY82Uuri+JZk>QKS3#}sRqppI=brY)+g5$?!8C$=8f>cS(mEWw_CK={4Xhl$ zfkjrcWJ0EX-6|Hr2X7d>H*3@~Z|utjCAzG=!LRe{QE$qT(M=$3yWy<(GN~?eW$)tj zs*F18?6j;i9&deqFT^`LLc#LUonf77a4zTHa{FI?+&OKPY7E*?-e%~LU)5WD4%9;b z!Nb;Tr#%6yV`4rL1!>&S8^^tZoGsN69SfI*g!EpN!G$r#iFa6;9mZQb->gq8*d3fg 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zK)R?sTryR$K|O1b4ZB(okHXmOOKnR{iknvh3I=UrU2`wl>). \itemize{ - \item \code{-e, -- extended} to output canonical, modified, and filtered bases; - \item \code{-m, -- mod_base=BASE} to output modified base of interest, one of: 5mC, 5hmC, 5fC, 5caC, 5hmU, 5fU, 5caU, 6mA, 5oxoG, Xao. (Or modA, modC, modG, modT, modU, modN for generic modified base); - \item \code{-r, --region=chr:start-end} to output chromosome or genomic region of interest; - \item \code{-f, --threshold=THRESHOLD} to output filtered bases for + \item \code{-e, -- extended} to output canonical, modified, and filtered bases; + \item \code{-m, -- mod_base=BASE} to output modified base of interest, one of: 5mC, 5hmC, 5fC, 5caC, 5hmU, 5fU, 5caU, 6mA, 5oxoG, Xao. (Or modA, modC, modG, modT, modU, modN for generic modified base); + \item \code{-r, --region=chr:start-end} to output chromosome or genomic region of interest; + \item \code{-f, --threshold=THRESHOLD} to output filtered bases for probability lower than threshold (default = 0.66) } } \subsection{modbam2bed to Bsseq object}{ - After creating BED files using modbam2bed, the BED files are read in and the Bsseq object is constructed via \code{read.modbam2bed()} function. The function reads in BED files, extract genomic regions, methylation, coverage, ambiguous modification status data and sample information and then construct Bsseq object using \code{BSseq} function within the package.} + After creating BED files using modbam2bed, the BED files are read in and the Bsseq object is constructed via \code{read.modbam2bed()} function. The function reads in BED files, extract genomic regions, methylation, coverage, ambiguous modification status data and sample information and then construct Bsseq object using \code{BSseq} function within the package.} } \examples{ -files <- c(system.file("extdata/modbam2bed/Ctr1.bed.gz", package = "bsseq"), - system.file("extdata/modbam2bed/Ctr2.bed.gz", package = "bsseq"), - system.file("extdata/modbam2bed/Ctr3.bed.gz", package = "bsseq"), - system.file("extdata/modbam2bed/Tret1.bed.gz", package = "bsseq"), - system.file("extdata/modbam2bed/Tret2.bed.gz", package = "bsseq"), - system.file("extdata/modbam2bed/Tret3.bed.gz", package = "bsseq")) +files <- c(system.file("extdata/modbam2bed/ctr1.chr10.chr11.bed.gz", package = "bsseq"), + system.file("extdata/modbam2bed/ctr2.chr10.chr11.bed.gz", package = "bsseq"), + system.file("extdata/modbam2bed/ctr3.chr10.chr11.bed.gz", package = "bsseq"), + system.file("extdata/modbam2bed/tret1.chr10.chr11.bed.gz", package = "bsseq"), + system.file("extdata/modbam2bed/tret2.chr10.chr11.bed.gz", package = "bsseq"), + system.file("extdata/modbam2bed/tret3.chr10.chr11.bed.gz", package = "bsseq")) pd <- data.frame(condition = rep(c("control", "treatment"), each = 3), - replicate = rep(c("rep1", "rep2", "rep3"), times = 2)) + replicate = rep(c("rep1", "rep2", "rep3"), times = 2)) bsseq_nano <- bsseq::read.modbam2bed(files,colData=pd,rmZeroCov = FALSE, - strandCollapse=TRUE) + strandCollapse=TRUE) } diff --git a/man/read.modkit.Rd b/man/read.modkit.Rd index 41ef0ab..c4e14e9 100644 --- a/man/read.modkit.Rd +++ b/man/read.modkit.Rd @@ -6,17 +6,17 @@ Construct BSseq objects from nanopore BED files } \usage{ read.modkit( - files, - colData = NULL, - rmZeroCov = FALSE, - strandCollapse = TRUE + files, + colData = NULL, + rmZeroCov = FALSE, + strandCollapse = TRUE ) } \arguments{ - \item{files}{vector, BED files} - \item{colData}{data frame, phenotypic data with samples as rows and variables as columns} - \item{rmZeroCov}{A logical (1) indicating whether methylation loci that have zero coverage in all samples be removed} - \item{strandCollapse}{A logical (1) indicating whether stand-symmetric methylation loci (i.e. CpGs) should be collapsed across strands} + \item{files}{vector, BED files} + \item{colData}{data frame, phenotypic data with samples as rows and variables as columns} + \item{rmZeroCov}{A logical (1) indicating whether methylation loci that have zero coverage in all samples be removed} + \item{strandCollapse}{A logical (1) indicating whether stand-symmetric methylation loci (i.e. CpGs) should be collapsed across strands} } \value{ @@ -29,10 +29,10 @@ counts) is stored in modified-base BAM files. These modified-base BAM files are converted to bedMethyl (BED) files using \href{https://github.com/nanoporetech/modkit}{modkit}. \subsection{Details for modkit}{ - Modkit outputs modified reads, unmodified reads, ambiguous modification reads (reads where the probability was below the threshold and usually failing the lowest 10th percentile), and other modified reads.} + Modkit outputs modified reads, unmodified reads, ambiguous modification reads (reads where the probability was below the threshold and usually failing the lowest 10th percentile), and other modified reads.} \subsection{modkit to Bsseq object}{ - After creating BED files using modkit, the BED files are read in and the Bsseq object is constructed via \code{read.modkit()} function. The function reads in BED files, extract genomic regions, methylation, coverage, ambiguous modification status data and sample information and then construct Bsseq object using \code{BSseq} function within the package. If there are other modified reads, two Bsseq objects are constructed with the first one using major modified reads and their corresponding coverage and the second one using the other modified reads and their corresponding coverage.} + After creating BED files using modkit, the BED files are read in and the Bsseq object is constructed via \code{read.modkit()} function. The function reads in BED files, extract genomic regions, methylation, coverage, ambiguous modification status data and sample information and then construct Bsseq object using \code{BSseq} function within the package. If there are other modified reads, two Bsseq objects are constructed with the first one using major modified reads and their corresponding coverage and the second one using the other modified reads and their corresponding coverage.} } \examples{ diff --git a/tests/testthat/test_read.modbam2bed.R b/tests/testthat/test_read.modbam2bed.R index 9ad6a82..5e5eb10 100644 --- a/tests/testthat/test_read.modbam2bed.R +++ b/tests/testthat/test_read.modbam2bed.R @@ -2,7 +2,7 @@ context("read.modbam2bed") # TODO: Re-factor read.modbam2bed() and update tests accordingly test_that("read.modbam2bed() works for BED files", { - infile <- system.file("extdata", "modbam2bed/Ctr1.bed.gz",package = "bsseq") + infile <- system.file("extdata", "modbam2bed/ctr1.chr10.chr11.bed.gz",package = "bsseq") bsseq <- read.modbam2bed(files = infile, colData = NULL, rmZeroCov = FALSE,