countRangeset {systemPipeR} | R Documentation

## Read counting for several range sets

### Description

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.

### Usage

    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(s)

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)
    bfl <- BamFileList(outpaths(args_bam), yieldSize=50000, index=character())

    ## Not run:
    ##########################################
    ## 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)

    ## End(Not run)

[Package systemPipeR version 2.0.8 Index]