Read counting for several range sets

Convenience function to perform read counting iteratively for serveral range sets, e.g. peak range sets or feature types. Internally, the read counting is performed with the summarizeOverlaps function from the GenomicAlignments package. The resulting count tables are directly saved to files.

countRangeset(bfl, args, outfiles=NULL, format="tabular", ...)

Arguments

bfl

BamFileList object containing paths to one or more BAM files.

args

An instance of SYSargs or SYSargs2 constructed from a targets file where the first column (targetsin(args) or targets.as.df(targets(args))) contains the paths to the tabular range data files (e.g. peak ranges) used for counting. Another possibily is named character vector with the paths to the tabular range data files and the elements names should be the sampleID.

outfiles

Default is NULL. When args is an object of named character vector class, outfile argument is required. Named character vector with the paths to the resulting count tables and the elements names should be the sampleID.

format

Format of input range files. Currently, supported are tabular or bed. If tabular is selected then the input range files need to contain the proper column titles to coerce with as(..., "GRanges") to GRanges objects after importing them with read.delim. The latter is the case for the peak files (*peaks.xls) generated by the MACS2 software.

...

Arguments to be passed on to internally used summarizeOverlaps function.

Value

Named character vector containing the paths from outpaths(args) to the resulting count table files.

Author

Thomas Girke

See also

summarizeOverlaps

Examples

## Paths to BAM files
param <- system.file("extdata", "bowtieSE.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args_bam <- systemArgs(sysma=param, mytargets=targets)
#> Warning: path[1]="./data/SRR446027_1.fastq.gz": No such file or directory
#> Warning: path[2]="./data/SRR446028_1.fastq.gz": No such file or directory
#> Warning: path[3]="./data/SRR446029_1.fastq.gz": No such file or directory
#> Warning: path[4]="./data/SRR446030_1.fastq.gz": No such file or directory
#> Warning: path[5]="./data/SRR446031_1.fastq.gz": No such file or directory
#> Warning: path[6]="./data/SRR446032_1.fastq.gz": No such file or directory
#> Warning: path[7]="./data/SRR446033_1.fastq.gz": No such file or directory
#> Warning: path[8]="./data/SRR446034_1.fastq.gz": No such file or directory
#> Warning: path[9]="./data/SRR446035_1.fastq.gz": No such file or directory
#> Warning: path[10]="./data/SRR446036_1.fastq.gz": No such file or directory
#> Warning: path[11]="./data/SRR446037_1.fastq.gz": No such file or directory
#> Warning: path[12]="./data/SRR446038_1.fastq.gz": No such file or directory
#> Warning: path[13]="./data/SRR446039_1.fastq.gz": No such file or directory
#> Warning: path[14]="./data/SRR446040_1.fastq.gz": No such file or directory
#> Warning: path[15]="./data/SRR446041_1.fastq.gz": No such file or directory
#> Warning: path[16]="./data/SRR446042_1.fastq.gz": No such file or directory
#> Warning: path[17]="./data/SRR446043_1.fastq.gz": No such file or directory
#> Warning: path[18]="./data/SRR446044_1.fastq.gz": No such file or directory
bfl <- BamFileList(outpaths(args_bam), yieldSize=50000, index=character())

if (FALSE) {
##########################################
## Examples with \code{SYSargs2} object ##
##########################################
## Construct SYSargs2 object 
## SYSargs2 with paths to range data and count files
dir_path <- system.file("extdata/cwl/count_rangesets", package="systemPipeR")
args <- loadWF(targets = "targets_macs.txt", wf_file = "count_rangesets.cwl", 
    input_file = "count_rangesets.yml", dir_path = dir_path)
args <- renderWF(args, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))

## Iterative read counting
countDFnames <- countRangeset(bfl, args, mode="Union", ignore.strand=TRUE)

##########################################
## Examples with \code{SYSargs} object ##
##########################################
## Construct SYSargs object 
## SYSargs with paths to range data and count files
args <- systemArgs(sysma="param/count_rangesets.param", mytargets="targets_macs.txt")

## Iterative read counting
countDFnames <- countRangeset(bfl, args, mode="Union", ignore.strand=TRUE)
writeTargetsout(x=args, file="targets_countDF.txt", overwrite=TRUE)
}