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R/writeTSS.R
In TSRchitect: Promoter identification from large-scale TSS profiling data
#' @title \strong{writeTSS}
#'
#' @description \code{writeTSS} writes identified TSSs
#' from a specified data set to a file in either tab or BED formats
#'
#' @param experimentName an S4 object of class \emph{tssObject} containing
#' information in slot \emph{@@tssCountData}
#' @param tssSetType specifies the set to be written to file.
#' Options are "replicates" or "merged". (character)
#' @param tssSet number of the dataset to be processed (numeric).
#' @param tssLabel specifies the label to be used in the name column of
#' BED format output
#' @param mixedorder a logical specifying whether the sequence names should
#' be ordered alphanumerically ("10" following "9" rather than "1"). (logical)
#' @param fileType the format of the file to be written.
#' Possible choices are "tab" for tab-delimited output, "bed" for BED format,
#' and "bedGraph" for BedGraph format (character). In case "bedGraph," three
#' output files are produced: *_PLUS.bedGraph and *_MINUS.bedGraph, which
#' record the number of TSS tags per position on plus and minus strand
#' separately; and a combined *.bedGraph file which lists plus strand tag
#' counts as positive numbers, minus strand tag counts as negative numbers,
#' and positions with both plus and minus strand tag counts display the
#' tag count corresponding to the highest absolute value.
#'
#' @return A table containing the specified TSS data set that
#' is to be written to your working directory.
#'
#' @import BiocGenerics
#' @importFrom gtools mixedorder
#' @importFrom rtracklayer export.bed
#'
#' @examples
#' load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect"))
#' writeTSS(experimentName=tssObjectExample, tssSetType="replicates",
#' tssSet=1, tssLabel="TSSsample1_", mixedorder=FALSE, fileType="tab")
#'
#' @note The .bed file written adheres to the standard six-column BED format,
#' while "tab" format is identical to that of the data.frames containing TSS
#' data.
#' @note For more information on the BED format, please visit
#' https://genome.ucsc.edu/FAQ/FAQformat#format1
#'
#' @export
#' @rdname writeTSS-methods
setGeneric("writeTSS",
function(experimentName, tssSetType, tssSet=1, tssLabel="TSS_",
mixedorder=FALSE, fileType="tab")
standardGeneric("writeTSS")
)
#' @rdname writeTSS-methods
setMethod("writeTSS",
signature(experimentName="tssObject", "character", "numeric",
"character", "logical", "character"),
function(experimentName, tssSetType, tssSet,
tssLabel, mixedorder, fileType) {
message("... writeTSS ...")
if (tssSetType=="replicates") {
if (tssSet>length(experimentName@tssCountData)) {
stop("The value selected for tssSet exceeds the",
" number of slots in tssCountData.")
}
outfname <- paste("TSSset-", tssSet, sep="")
if (fileType == "tab") {
outfname <- paste(outfname, "tab", sep=".")
} else if (fileType == "bed") {
outfname <- paste(outfname, "bed", sep=".")
} else if (fileType == "bedGraph") {
outfname <- paste(outfname, "bedGraph", sep=".")
} else {
stop("Unknown fileType selected for writeTSS.",
" Please check.")
}
message("\nThe TSS set for TSS dataset ", tssSet,
" will be written to file ",
outfname, "\nin your working directory.")
if (!missing(mixedorder) & mixedorder == TRUE) {
tss.df <- experimentName@tssCountData[[tssSet]][mixedorder(
experimentName@tssCountData[[tssSet]]$seq),]
} else {
tss.df <- experimentName@tssCountData[[tssSet]]
}
} else if (tssSetType=="merged") {
if (length(experimentName@tssCountDataMerged)<1) {
stop("The @tssCountDataMerged slot is currently empty.",
" Please complete the merger before continuing.")
}
if (tssSet>length(experimentName@tssCountDataMerged)) {
stop("The value selected for tssSet exceeds the",
" number of slots in tssCountDataMerged.")
}
if (tssSet<length(experimentName@tssCountDataMerged)) {
outfname <- paste("TSSsetMerged-", tssSet, sep="")
if (fileType == "tab") {
outfname <- paste(outfname, "tab", sep=".")
} else if (fileType == "bed") {
outfname <- paste(outfname, "bed", sep=".")
} else if (fileType == "bedGraph") {
outfname <- paste(outfname, "bedGraph", sep=".")
} else {
stop("Unknown fileType selected for writeTSS.",
" Please check.")
}
message("\nThe merged TSS set for TSS dataset ", tssSet,
" will be written to file ", outfname,
"\nin your working directory.")
} else { # "combined" case
if (fileType == "tab") {
outfname <- "TSSsetCombined.tab"
} else if (fileType == "bed") {
outfname <- "TSSsetCombined.bed"
} else if (fileType == "bedGraph") {
outfname <- "TSSsetCombined.bedGraph"
} else {
stop("Unknown fileType selected for writeTSS.",
" Please check.")
}
message("\nThe combined TSS set derived from all samples",
" will be written to file ", outfname,
"\nin your working directory.")
}
if (!missing(mixedorder) & mixedorder == TRUE) {
tss.df <- experimentName@tssCountDataMerged[[tssSet]][mixedorder(
experimentName@tssCountDataMerged[[tssSet]]$seq),]
} else {
tss.df <- experimentName@tssCountDataMerged[[tssSet]]
}
} else {
stop("Error: argument tssSetType to writeTSS() should be",
" either \"replicates\" or \"merged\".")
}
if (fileType == "tab") {
write.table(format(tss.df,scientific=FALSE), file=outfname,
col.names=FALSE, row.names=FALSE, sep="\t",
quote=FALSE)
} else if (fileType == "bed") {
tss.df$ID <- paste(tssLabel,which(tss.df$seq != ""),sep="_")
out.df <- tss.df[, c("seq", "TSS", "TSS", "ID",
"nTAGs", "strand")]
colnames(out.df) <- c("chrom", "start", "end", "name",
"score", "strand")
export.bed(out.df,con=outfname)
} else { # fileType == "bedGraph")
tss.df$beg <- tss.df$TSS -1;
tssP.df <- tss.df[tss.df$strand=="+",
c("seq", "beg", "TSS", "nTAGs")]
write.table(format(tssP.df,scientific=FALSE,trim=TRUE),
file=sub(".bedGraph","_PLUS.bedGraph",outfname),
col.names=FALSE, row.names=FALSE,
sep="\t", quote=FALSE)
tssM.df <- tss.df[tss.df$strand=="-",
c("seq", "beg", "TSS", "nTAGs")]
write.table(format(tssM.df,scientific=FALSE,trim=TRUE),
file=sub(".bedGraph","_MINUS.bedGraph",outfname),
col.names=FALSE, row.names=FALSE,
sep="\t", quote=FALSE)
tss.df$score[tss.df$strand=="+"] <-
tss.df$nTAGs[tss.df$strand=="+"]
tss.df$score[tss.df$strand=="-"] <-
-tss.df$nTAGs[tss.df$strand=="-"]
# ... bigWig (a common way to display bedGraph files) does not
# tolerate overlapping regions, thus we record only the
# maximal tag count in a position that is recorded both on the
# plus and the minus strand (presumably a rare event ...):
tmptssdf <- tss.df[,c("seq","beg")]
i1 <- row.names(tmptssdf[duplicated(tmptssdf),])
i2 <- row.names(tmptssdf[duplicated(tmptssdf,fromLast=TRUE),])
j1 <- ifelse (abs(tss.df[i1,"score"])
< abs(tss.df[i2,"score"]),i1,i2)
j2 <- ifelse (abs(tss.df[i1,"score"])
>= abs(tss.df[i2,"score"]),i1,i2)
tss.df[j1,] <- tss.df[j2,]
tss.df <- tss.df[!duplicated(tss.df),]
out.df <- tss.df[with(tss.df,order(tss.df$seq,tss.df$beg)),
c("seq", "beg", "TSS", "score")]
write.table(format(out.df,scientific=FALSE,trim=TRUE),
file=outfname, col.names=FALSE, row.names=FALSE,
sep="\t", quote=FALSE)
}
message("---------------------------------------------------------\n")
message(" Done.\n")
}
)
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#' @title \strong{writeTSS}
#'
#' @description \code{writeTSS} writes identified TSSs
#' from a specified data set to a file in either tab or BED formats
#'
#' @param experimentName an S4 object of class \emph{tssObject} containing
#' information in slot \emph{@@tssCountData}
#' @param tssSetType specifies the set to be written to file.
#' Options are "replicates" or "merged". (character)
#' @param tssSet number of the dataset to be processed (numeric).
#' @param tssLabel specifies the label to be used in the name column of
#' BED format output
#' @param mixedorder a logical specifying whether the sequence names should
#' be ordered alphanumerically ("10" following "9" rather than "1"). (logical)
#' @param fileType the format of the file to be written.
#' Possible choices are "tab" for tab-delimited output, "bed" for BED format,
#' and "bedGraph" for BedGraph format (character). In case "bedGraph," three
#' output files are produced: *_PLUS.bedGraph and *_MINUS.bedGraph, which
#' record the number of TSS tags per position on plus and minus strand
#' separately; and a combined *.bedGraph file which lists plus strand tag
#' counts as positive numbers, minus strand tag counts as negative numbers,
#' and positions with both plus and minus strand tag counts display the
#' tag count corresponding to the highest absolute value.
#'
#' @return A table containing the specified TSS data set that
#' is to be written to your working directory.
#'
#' @import BiocGenerics
#' @importFrom gtools mixedorder
#' @importFrom rtracklayer export.bed
#'
#' @examples
#' load(system.file("extdata", "tssObjectExample.RData", package="TSRchitect"))
#' writeTSS(experimentName=tssObjectExample, tssSetType="replicates",
#' tssSet=1, tssLabel="TSSsample1_", mixedorder=FALSE, fileType="tab")
#'
#' @note The .bed file written adheres to the standard six-column BED format,
#' while "tab" format is identical to that of the data.frames containing TSS
#' data.
#' @note For more information on the BED format, please visit
#' https://genome.ucsc.edu/FAQ/FAQformat#format1
#'
#' @export
#' @rdname writeTSS-methods
setGeneric("writeTSS",
function(experimentName, tssSetType, tssSet=1, tssLabel="TSS_",
mixedorder=FALSE, fileType="tab")
standardGeneric("writeTSS")
)
#' @rdname writeTSS-methods
setMethod("writeTSS",
signature(experimentName="tssObject", "character", "numeric",
"character", "logical", "character"),
function(experimentName, tssSetType, tssSet,
tssLabel, mixedorder, fileType) {
message("... writeTSS ...")
if (tssSetType=="replicates") {
if (tssSet>length(experimentName@tssCountData)) {
stop("The value selected for tssSet exceeds the",
" number of slots in tssCountData.")
}
outfname <- paste("TSSset-", tssSet, sep="")
if (fileType == "tab") {
outfname <- paste(outfname, "tab", sep=".")
} else if (fileType == "bed") {
outfname <- paste(outfname, "bed", sep=".")
} else if (fileType == "bedGraph") {
outfname <- paste(outfname, "bedGraph", sep=".")
} else {
stop("Unknown fileType selected for writeTSS.",
" Please check.")
}
message("\nThe TSS set for TSS dataset ", tssSet,
" will be written to file ",
outfname, "\nin your working directory.")
if (!missing(mixedorder) & mixedorder == TRUE) {
tss.df <- experimentName@tssCountData[[tssSet]][mixedorder(
experimentName@tssCountData[[tssSet]]$seq),]
} else {
tss.df <- experimentName@tssCountData[[tssSet]]
}
} else if (tssSetType=="merged") {
if (length(experimentName@tssCountDataMerged)<1) {
stop("The @tssCountDataMerged slot is currently empty.",
" Please complete the merger before continuing.")
}
if (tssSet>length(experimentName@tssCountDataMerged)) {
stop("The value selected for tssSet exceeds the",
" number of slots in tssCountDataMerged.")
}
if (tssSet<length(experimentName@tssCountDataMerged)) {
outfname <- paste("TSSsetMerged-", tssSet, sep="")
if (fileType == "tab") {
outfname <- paste(outfname, "tab", sep=".")
} else if (fileType == "bed") {
outfname <- paste(outfname, "bed", sep=".")
} else if (fileType == "bedGraph") {
outfname <- paste(outfname, "bedGraph", sep=".")
} else {
stop("Unknown fileType selected for writeTSS.",
" Please check.")
}
message("\nThe merged TSS set for TSS dataset ", tssSet,
" will be written to file ", outfname,
"\nin your working directory.")
} else { # "combined" case
if (fileType == "tab") {
outfname <- "TSSsetCombined.tab"
} else if (fileType == "bed") {
outfname <- "TSSsetCombined.bed"
} else if (fileType == "bedGraph") {
outfname <- "TSSsetCombined.bedGraph"
} else {
stop("Unknown fileType selected for writeTSS.",
" Please check.")
}
message("\nThe combined TSS set derived from all samples",
" will be written to file ", outfname,
"\nin your working directory.")
}
if (!missing(mixedorder) & mixedorder == TRUE) {
tss.df <- experimentName@tssCountDataMerged[[tssSet]][mixedorder(
experimentName@tssCountDataMerged[[tssSet]]$seq),]
} else {
tss.df <- experimentName@tssCountDataMerged[[tssSet]]
}
} else {
stop("Error: argument tssSetType to writeTSS() should be",
" either \"replicates\" or \"merged\".")
}
if (fileType == "tab") {
write.table(format(tss.df,scientific=FALSE), file=outfname,
col.names=FALSE, row.names=FALSE, sep="\t",
quote=FALSE)
} else if (fileType == "bed") {
tss.df$ID <- paste(tssLabel,which(tss.df$seq != ""),sep="_")
out.df <- tss.df[, c("seq", "TSS", "TSS", "ID",
"nTAGs", "strand")]
colnames(out.df) <- c("chrom", "start", "end", "name",
"score", "strand")
export.bed(out.df,con=outfname)
} else { # fileType == "bedGraph")
tss.df$beg <- tss.df$TSS -1;
tssP.df <- tss.df[tss.df$strand=="+",
c("seq", "beg", "TSS", "nTAGs")]
write.table(format(tssP.df,scientific=FALSE,trim=TRUE),
file=sub(".bedGraph","_PLUS.bedGraph",outfname),
col.names=FALSE, row.names=FALSE,
sep="\t", quote=FALSE)
tssM.df <- tss.df[tss.df$strand=="-",
c("seq", "beg", "TSS", "nTAGs")]
write.table(format(tssM.df,scientific=FALSE,trim=TRUE),
file=sub(".bedGraph","_MINUS.bedGraph",outfname),
col.names=FALSE, row.names=FALSE,
sep="\t", quote=FALSE)
tss.df$score[tss.df$strand=="+"] <-
tss.df$nTAGs[tss.df$strand=="+"]
tss.df$score[tss.df$strand=="-"] <-
-tss.df$nTAGs[tss.df$strand=="-"]
# ... bigWig (a common way to display bedGraph files) does not
# tolerate overlapping regions, thus we record only the
# maximal tag count in a position that is recorded both on the
# plus and the minus strand (presumably a rare event ...):
tmptssdf <- tss.df[,c("seq","beg")]
i1 <- row.names(tmptssdf[duplicated(tmptssdf),])
i2 <- row.names(tmptssdf[duplicated(tmptssdf,fromLast=TRUE),])
j1 <- ifelse (abs(tss.df[i1,"score"])
< abs(tss.df[i2,"score"]),i1,i2)
j2 <- ifelse (abs(tss.df[i1,"score"])
>= abs(tss.df[i2,"score"]),i1,i2)
tss.df[j1,] <- tss.df[j2,]
tss.df <- tss.df[!duplicated(tss.df),]
out.df <- tss.df[with(tss.df,order(tss.df$seq,tss.df$beg)),
c("seq", "beg", "TSS", "score")]
write.table(format(out.df,scientific=FALSE,trim=TRUE),
file=outfname, col.names=FALSE, row.names=FALSE,
sep="\t", quote=FALSE)
}
message("---------------------------------------------------------\n")
message(" Done.\n")
}
)
Try the TSRchitect package in your browser
Any scripts or data that you put into this service are public.
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