R/loadTSSobj.R
In BrendelGroup/TSRchitect: Promoter identification from large-scale TSS profiling data
#' @title \strong{loadTSSobj}
#' @description \code{loadTSSobj} processes alignment files in .bam or .bed
#' formats from the local directory supplied.
#'
#' @param experimentTitle a descriptive title for the experiment (character).
#' @param inputDir path to the directory containing the alignment files (in
#' either .bam or .bed formats) (character).
#' Note that all the paths to all files in \emph{inputDir} with the extension
#' .bam or .bed will be imported with this function.
#' @param n.cores the number of cores to be used for this job. (numeric)
#' @param isPairedBAM if the input is in BAM format, specifies whether the
#' TSS profiling experiment is paired-end (if TRUE) or single-end
#' (if FALSE). Set to TRUE by default. (logical)
#' @param isPairedBED if the input is in BED format, specifies whether the
#' TSS profiling experiment is paired-end (if TRUE) or single-end
#' (if FALSE). Set to TRUE by default. (logical)
#' Note: if TRUE, the input data must be in bedpe format, as described here:
#' http://bedtools.readthedocs.io/en/latest/content/general-usage.html
#' @param sampleSheet file providing TSS sample information; if provided,
#' sampleNames and replicateIDs are ignored; input format is tab-delimited
#' 3-column rows with sample name, replicate ID, and sample data file name;
#' the file has to include column headers "SAMPLE ReplicateID FILE"
#' and can be either tab-delimited or an Excel spreadsheet (file extension
#' ".xls" or "xlsx" (character)
#' @param sampleNames unique labels of class character for each TSS sample
#' within the experiment (character).
#' @param replicateIDs identifiers indicating which samples are biological
#' replicates. Note that \code{loadTSSobj} imports alignment data in ascending
#' alphanumeric order, so the arguments to replicateIDs must be arranged in this
#' order also so that they directly correspond to the intended file.
#' Thus replicateIDs must be ordinal values in consecutive order without gaps
#' (e.g. 1, 2, 3, ...) (numeric).
#' @return \emph{loadTSSobj} fills the slot \emph{bamDataFirstRead} and/or \emph{bedData}
#' on the returned \emph{tssObject} with \linkS4class{GAlignments} objects
#' (for .bam files), or \linkS4class{GRanges} objects (for .bed files).
#'
#' @importFrom BiocParallel bplapply MulticoreParam
#' @importFrom GenomicAlignments readGAlignments
#' @importFrom Rsamtools scanBamFlag ScanBamParam BamViews
#' @importFrom methods new
#' @importFrom readxl read_excel
#' @importFrom rtracklayer import import.bed
#' @importFrom tools file_ext
#' @importFrom utils read.table
#'
#' @examples
#' extdata.dir <- system.file("extdata/bamFiles", package="TSRchitect")
#' test.Obj <- loadTSSobj(experimentTitle="Code example", inputDir=extdata.dir,
#' n.cores=2, isPairedBAM=TRUE, sampleNames=c("sample1-rep1", "sample1-rep2",
#' "sample2-rep1","sample2-rep2"), replicateIDs=c(1,1,2,2))
#'
#' @note An example similar to the one provided can be found in
#' the vignette (/inst/doc/TSRchitect.Rmd).
#' @note All files found in \emph{inputDir} will be
#' retrieved and written in ascending alphanumeric order to the
#' \emph{@fileNamesBAM} and/or \emph{@fileNamesBED} slot(s) on
#' the \emph{tssObject} that is created.
#'
#' @export
#' @rdname loadTSSobj-methods
setGeneric("loadTSSobj",
function(experimentTitle, inputDir, ...)
standardGeneric("loadTSSobj")
)
#' @rdname loadTSSobj-methods
setMethod("loadTSSobj",
signature(experimentTitle="character", inputDir="character"),
function(experimentTitle, inputDir, n.cores=1,
isPairedBAM=TRUE, isPairedBED=TRUE,
sampleSheet=NA, sampleNames=NA, replicateIDs=NA) {
message("... loadTSSobj ...")
tssObj <- new("tssObject")
tssObj@title <- experimentTitle
tss_filesBAM <- vector(mode="character",length=0)
tss_filesBED <- vector(mode="character",length=0)
if(!missing(sampleSheet) & is.character(sampleSheet)) {
sampleSheet <- file.path(inputDir,sampleSheet)
ext <- file_ext(sampleSheet)
if (ext %in% c("xls","xlsx")) {
samples <- read_excel(sampleSheet)
} else {
samples <- read.table(sampleSheet,sep=' ',
stringsAsFactors=F,header=T,
comment.char="")
}
sampleNames <- samples$SAMPLE
replicateIDs <- samples$ReplicateID
for (file in samples$FILE) {
ext <- file_ext(file)
if (ext %in% c("bam","Bam")) {
tss_filesBAM <- c(tss_filesBAM,file)
} else if (ext %in% c("bed","Bed")) {
tss_filesBED <- c(tss_filesBED,file)
} else {
message("No .bam nor .bed files specified in ",sampleSheet);
message("Please check your input file.")
}
}
}
if (anyNA(sampleNames) | !is.character(sampleNames) |
anyNA(replicateIDs) | !is.numeric(replicateIDs) ) {
stop("You must specify both sample names (as \"character\")",
" and replicate IDs (as \"numeric\"). Please check.")
}
if (!missing(n.cores) & n.cores > 1) {
BiocParallel::register(MulticoreParam(workers=n.cores),
default=TRUE)
}
if (isPairedBAM==TRUE) {
tssObj@dataTypeBAM <- c("pairedEnd")
}
if (isPairedBAM==FALSE) {
tssObj@dataTypeBAM <- c("singleEnd")
}
if (isPairedBED==TRUE) {
tssObj@dataTypeBED <- c("pairedEnd")
}
if (isPairedBED==FALSE) {
tssObj@dataTypeBED <- c("singleEnd")
}
if (length(tss_filesBAM) == 0) {
tss_filesBAM <- list.files(inputDir, pattern="\\.bam$",
all.files=FALSE, full.names=TRUE)
}
tssObj@fileNamesBAM <- tss_filesBAM
if (length(tss_filesBAM) > 0) {
if (is.character(tssObj@dataTypeBAM)==FALSE) {
stop("The argument 'isPairedBAM' is empty. Please fix.")
}
if (tssObj@dataTypeBAM=="singleEnd") {
message("\nImporting single-end reads ...\n")
bamFlags <- scanBamFlag(isPaired=FALSE,
isUnmappedQuery=FALSE,
isSecondaryAlignment=FALSE)
myFields <- c("rname","flag","pos", "qwidth","mapq",
"cigar","qname")
}
if (tssObj@dataTypeBAM=="pairedEnd") {
message("\nImporting paired-end reads (first reads) ...\n")
bamFlags <- scanBamFlag(isPaired=TRUE, isProperPair=TRUE,
isFirstMateRead=TRUE, hasUnmappedMate=FALSE,
isUnmappedQuery=FALSE,
isSecondaryAlignment=FALSE)
myFields <- c("rname","flag","pos","qwidth","mapq",
"cigar","isize","qname")
}
my.param <- ScanBamParam(flag=bamFlags, what=myFields)
bam.paths <- tssObj@fileNamesBAM
bv_obj <- BamViews(bam.paths)
bv_files <- dimnames(bv_obj)[[2]]
n.bams <- length(bv_files)
message("\nBeginning import of ", n.bams, " bam files ...\n")
if (!missing(n.cores) & n.cores > 1) {
bams.GA <- bplapply(bam.paths, readGAlignments,
BPPARAM = MulticoreParam(), param=my.param)
} else {
bams.GA <- lapply(bam.paths, readGAlignments, param=my.param)
}
tssObj@bamDataFirstRead <- bams.GA
if (tssObj@dataTypeBAM=="pairedEnd") {
message("\nImporting paired-end reads (last reads) ...\n")
bamFlags <- scanBamFlag(isPaired=TRUE, isProperPair=TRUE,
isFirstMateRead=FALSE, hasUnmappedMate=FALSE,
isUnmappedQuery=FALSE,
isSecondaryAlignment=FALSE)
my.param <- ScanBamParam(flag=bamFlags, what=myFields)
if (!missing(n.cores) & n.cores > 1) {
bams.GA <- bplapply(bam.paths, readGAlignments,
BPPARAM = MulticoreParam(), param=my.param)
} else {
bams.GA <- lapply(bam.paths, readGAlignments, param=my.param)
}
tssObj@bamDataLastRead <- bams.GA
}
message("Done. Alignment data from ", n.bams,
" bam files have been attached to the tssObject.\n")
message("-----------------------------------------------------\n")
}
if (length(tss_filesBED) == 0) {
tss_filesBED <- list.files(inputDir, pattern="\\.bed$",
all.files=FALSE, full.names=TRUE)
}
if (length(tss_filesBED) > 0) {
if (isPairedBED == TRUE) {
message("\nImporting paired-end reads ...\n")
tssObj@fileNamesBED <- tss_filesBED
n.beds <- length(tss_filesBED)
message("\nBeginning import of ", n.beds, " bed files ...\n")
if (missing(n.cores) | n.cores > 1) {
beds.GR <- bplapply(tss_filesBED, import, format="bedpe",
BPPARAM = MulticoreParam() )
} else {
beds.GR <- lapply(tss_filesBED, import, format="bedpe")
}
tssObj@bedData <- beds.GR
message("Done. Alignment data from ", n.beds,
" bed files have been attached to the tssObject.\n")
message("-----------------------------------------------------\n")
}
if (isPairedBED==FALSE) {
message("\nImporting single-end reads ...\n")
tssObj@fileNamesBED <- tss_filesBED
n.beds <- length(tss_filesBED)
message("\nBeginning import of ", n.beds, " bed files ...\n")
if (!missing(n.cores) & n.cores > 1) {
beds.GR <- bplapply(tss_filesBED, import.bed,
BPPARAM = MulticoreParam() )
} else {
beds.GR <- lapply(tss_filesBED, import.bed)
}
tssObj@bedData <- beds.GR
message("Done. Alignment data from ", n.beds,
" bed files have been attached to the tssObject.\n")
message("-----------------------------------------------------\n")
}
}
if (length(sampleNames)!=(length(tss_filesBAM) +
length(tss_filesBED) )) {
stop("\nNumber of sampleNames must be equal to",
" number of input files.\nPlease check.")
}
if (length(sampleNames)!=(length(replicateIDs))) {
stop("\nsampleNames and replicateIDs must have equal lengths.",
" Please check.")
}
s.uni <- unique(sampleNames)
if (length(s.uni)<length(sampleNames)) {
stop("\nEach sample name must be unique.")
}
tssObj@sampleNames <- sampleNames
tssObj@replicateIDs <- replicateIDs
exp.len <- length(replicateIDs)
rep.list <- vector(mode="list", length=exp.len)
tssObj@tsrData <- rep.list
message("\nNames and replicate IDs were successfully added",
" to the tssObject.\n\n")
message("-----------------------------------------------------\n")
message(" Done.\n")
return(tssObj)
}
)
BrendelGroup/TSRchitect documentation built on March 3, 2021, 1:45 a.m.
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#' @title \strong{loadTSSobj}
#' @description \code{loadTSSobj} processes alignment files in .bam or .bed
#' formats from the local directory supplied.
#'
#' @param experimentTitle a descriptive title for the experiment (character).
#' @param inputDir path to the directory containing the alignment files (in
#' either .bam or .bed formats) (character).
#' Note that all the paths to all files in \emph{inputDir} with the extension
#' .bam or .bed will be imported with this function.
#' @param n.cores the number of cores to be used for this job. (numeric)
#' @param isPairedBAM if the input is in BAM format, specifies whether the
#' TSS profiling experiment is paired-end (if TRUE) or single-end
#' (if FALSE). Set to TRUE by default. (logical)
#' @param isPairedBED if the input is in BED format, specifies whether the
#' TSS profiling experiment is paired-end (if TRUE) or single-end
#' (if FALSE). Set to TRUE by default. (logical)
#' Note: if TRUE, the input data must be in bedpe format, as described here:
#' http://bedtools.readthedocs.io/en/latest/content/general-usage.html
#' @param sampleSheet file providing TSS sample information; if provided,
#' sampleNames and replicateIDs are ignored; input format is tab-delimited
#' 3-column rows with sample name, replicate ID, and sample data file name;
#' the file has to include column headers "SAMPLE ReplicateID FILE"
#' and can be either tab-delimited or an Excel spreadsheet (file extension
#' ".xls" or "xlsx" (character)
#' @param sampleNames unique labels of class character for each TSS sample
#' within the experiment (character).
#' @param replicateIDs identifiers indicating which samples are biological
#' replicates. Note that \code{loadTSSobj} imports alignment data in ascending
#' alphanumeric order, so the arguments to replicateIDs must be arranged in this
#' order also so that they directly correspond to the intended file.
#' Thus replicateIDs must be ordinal values in consecutive order without gaps
#' (e.g. 1, 2, 3, ...) (numeric).
#' @return \emph{loadTSSobj} fills the slot \emph{bamDataFirstRead} and/or \emph{bedData}
#' on the returned \emph{tssObject} with \linkS4class{GAlignments} objects
#' (for .bam files), or \linkS4class{GRanges} objects (for .bed files).
#'
#' @importFrom BiocParallel bplapply MulticoreParam
#' @importFrom GenomicAlignments readGAlignments
#' @importFrom Rsamtools scanBamFlag ScanBamParam BamViews
#' @importFrom methods new
#' @importFrom readxl read_excel
#' @importFrom rtracklayer import import.bed
#' @importFrom tools file_ext
#' @importFrom utils read.table
#'
#' @examples
#' extdata.dir <- system.file("extdata/bamFiles", package="TSRchitect")
#' test.Obj <- loadTSSobj(experimentTitle="Code example", inputDir=extdata.dir,
#' n.cores=2, isPairedBAM=TRUE, sampleNames=c("sample1-rep1", "sample1-rep2",
#' "sample2-rep1","sample2-rep2"), replicateIDs=c(1,1,2,2))
#'
#' @note An example similar to the one provided can be found in
#' the vignette (/inst/doc/TSRchitect.Rmd).
#' @note All files found in \emph{inputDir} will be
#' retrieved and written in ascending alphanumeric order to the
#' \emph{@fileNamesBAM} and/or \emph{@fileNamesBED} slot(s) on
#' the \emph{tssObject} that is created.
#'
#' @export
#' @rdname loadTSSobj-methods
setGeneric("loadTSSobj",
function(experimentTitle, inputDir, ...)
standardGeneric("loadTSSobj")
)
#' @rdname loadTSSobj-methods
setMethod("loadTSSobj",
signature(experimentTitle="character", inputDir="character"),
function(experimentTitle, inputDir, n.cores=1,
isPairedBAM=TRUE, isPairedBED=TRUE,
sampleSheet=NA, sampleNames=NA, replicateIDs=NA) {
message("... loadTSSobj ...")
tssObj <- new("tssObject")
tssObj@title <- experimentTitle
tss_filesBAM <- vector(mode="character",length=0)
tss_filesBED <- vector(mode="character",length=0)
if(!missing(sampleSheet) & is.character(sampleSheet)) {
sampleSheet <- file.path(inputDir,sampleSheet)
ext <- file_ext(sampleSheet)
if (ext %in% c("xls","xlsx")) {
samples <- read_excel(sampleSheet)
} else {
samples <- read.table(sampleSheet,sep=' ',
stringsAsFactors=F,header=T,
comment.char="")
}
sampleNames <- samples$SAMPLE
replicateIDs <- samples$ReplicateID
for (file in samples$FILE) {
ext <- file_ext(file)
if (ext %in% c("bam","Bam")) {
tss_filesBAM <- c(tss_filesBAM,file)
} else if (ext %in% c("bed","Bed")) {
tss_filesBED <- c(tss_filesBED,file)
} else {
message("No .bam nor .bed files specified in ",sampleSheet);
message("Please check your input file.")
}
}
}
if (anyNA(sampleNames) | !is.character(sampleNames) |
anyNA(replicateIDs) | !is.numeric(replicateIDs) ) {
stop("You must specify both sample names (as \"character\")",
" and replicate IDs (as \"numeric\"). Please check.")
}
if (!missing(n.cores) & n.cores > 1) {
BiocParallel::register(MulticoreParam(workers=n.cores),
default=TRUE)
}
if (isPairedBAM==TRUE) {
tssObj@dataTypeBAM <- c("pairedEnd")
}
if (isPairedBAM==FALSE) {
tssObj@dataTypeBAM <- c("singleEnd")
}
if (isPairedBED==TRUE) {
tssObj@dataTypeBED <- c("pairedEnd")
}
if (isPairedBED==FALSE) {
tssObj@dataTypeBED <- c("singleEnd")
}
if (length(tss_filesBAM) == 0) {
tss_filesBAM <- list.files(inputDir, pattern="\\.bam$",
all.files=FALSE, full.names=TRUE)
}
tssObj@fileNamesBAM <- tss_filesBAM
if (length(tss_filesBAM) > 0) {
if (is.character(tssObj@dataTypeBAM)==FALSE) {
stop("The argument 'isPairedBAM' is empty. Please fix.")
}
if (tssObj@dataTypeBAM=="singleEnd") {
message("\nImporting single-end reads ...\n")
bamFlags <- scanBamFlag(isPaired=FALSE,
isUnmappedQuery=FALSE,
isSecondaryAlignment=FALSE)
myFields <- c("rname","flag","pos", "qwidth","mapq",
"cigar","qname")
}
if (tssObj@dataTypeBAM=="pairedEnd") {
message("\nImporting paired-end reads (first reads) ...\n")
bamFlags <- scanBamFlag(isPaired=TRUE, isProperPair=TRUE,
isFirstMateRead=TRUE, hasUnmappedMate=FALSE,
isUnmappedQuery=FALSE,
isSecondaryAlignment=FALSE)
myFields <- c("rname","flag","pos","qwidth","mapq",
"cigar","isize","qname")
}
my.param <- ScanBamParam(flag=bamFlags, what=myFields)
bam.paths <- tssObj@fileNamesBAM
bv_obj <- BamViews(bam.paths)
bv_files <- dimnames(bv_obj)[[2]]
n.bams <- length(bv_files)
message("\nBeginning import of ", n.bams, " bam files ...\n")
if (!missing(n.cores) & n.cores > 1) {
bams.GA <- bplapply(bam.paths, readGAlignments,
BPPARAM = MulticoreParam(), param=my.param)
} else {
bams.GA <- lapply(bam.paths, readGAlignments, param=my.param)
}
tssObj@bamDataFirstRead <- bams.GA
if (tssObj@dataTypeBAM=="pairedEnd") {
message("\nImporting paired-end reads (last reads) ...\n")
bamFlags <- scanBamFlag(isPaired=TRUE, isProperPair=TRUE,
isFirstMateRead=FALSE, hasUnmappedMate=FALSE,
isUnmappedQuery=FALSE,
isSecondaryAlignment=FALSE)
my.param <- ScanBamParam(flag=bamFlags, what=myFields)
if (!missing(n.cores) & n.cores > 1) {
bams.GA <- bplapply(bam.paths, readGAlignments,
BPPARAM = MulticoreParam(), param=my.param)
} else {
bams.GA <- lapply(bam.paths, readGAlignments, param=my.param)
}
tssObj@bamDataLastRead <- bams.GA
}
message("Done. Alignment data from ", n.bams,
" bam files have been attached to the tssObject.\n")
message("-----------------------------------------------------\n")
}
if (length(tss_filesBED) == 0) {
tss_filesBED <- list.files(inputDir, pattern="\\.bed$",
all.files=FALSE, full.names=TRUE)
}
if (length(tss_filesBED) > 0) {
if (isPairedBED == TRUE) {
message("\nImporting paired-end reads ...\n")
tssObj@fileNamesBED <- tss_filesBED
n.beds <- length(tss_filesBED)
message("\nBeginning import of ", n.beds, " bed files ...\n")
if (missing(n.cores) | n.cores > 1) {
beds.GR <- bplapply(tss_filesBED, import, format="bedpe",
BPPARAM = MulticoreParam() )
} else {
beds.GR <- lapply(tss_filesBED, import, format="bedpe")
}
tssObj@bedData <- beds.GR
message("Done. Alignment data from ", n.beds,
" bed files have been attached to the tssObject.\n")
message("-----------------------------------------------------\n")
}
if (isPairedBED==FALSE) {
message("\nImporting single-end reads ...\n")
tssObj@fileNamesBED <- tss_filesBED
n.beds <- length(tss_filesBED)
message("\nBeginning import of ", n.beds, " bed files ...\n")
if (!missing(n.cores) & n.cores > 1) {
beds.GR <- bplapply(tss_filesBED, import.bed,
BPPARAM = MulticoreParam() )
} else {
beds.GR <- lapply(tss_filesBED, import.bed)
}
tssObj@bedData <- beds.GR
message("Done. Alignment data from ", n.beds,
" bed files have been attached to the tssObject.\n")
message("-----------------------------------------------------\n")
}
}
if (length(sampleNames)!=(length(tss_filesBAM) +
length(tss_filesBED) )) {
stop("\nNumber of sampleNames must be equal to",
" number of input files.\nPlease check.")
}
if (length(sampleNames)!=(length(replicateIDs))) {
stop("\nsampleNames and replicateIDs must have equal lengths.",
" Please check.")
}
s.uni <- unique(sampleNames)
if (length(s.uni)<length(sampleNames)) {
stop("\nEach sample name must be unique.")
}
tssObj@sampleNames <- sampleNames
tssObj@replicateIDs <- replicateIDs
exp.len <- length(replicateIDs)
rep.list <- vector(mode="list", length=exp.len)
tssObj@tsrData <- rep.list
message("\nNames and replicate IDs were successfully added",
" to the tssObject.\n\n")
message("-----------------------------------------------------\n")
message(" Done.\n")
return(tssObj)
}
)
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