regionCounts: Count reads overlapping each region

In LTLA/csaw: ChIP-Seq Analysis with Windows

Count reads overlapping each region

Description

Count the number of extended reads overlapping pre-specified regions

Usage

regionCounts(bam.files, regions, ext=100, param=readParam(),
    BPPARAM=SerialParam())

Arguments

bam.files	A character vector containing paths to sorted and indexed BAM files. Alternatively, a list of BamFile objects.
regions	A GenomicRanges object containing the regions over which reads are to be counted.
ext	An integer scalar or list describing the average length of the sequenced fragment in each library, see ?windowCounts.
param	A readParam object containing read extraction parameters, or a list of such objects (one for each BAM file).
BPPARAM	A BiocParallelParam specifying how parallelization is to be performed across files.

Details

This function simply provides a wrapper around countOverlaps for read counting into specified regions. It is provided so as to allow for counting with awareness of the other parameters, e.g., ext, pe. This allows users to coordinate region-based counts with those from windowCounts. Checking that the output totals are the same between the two calls is strongly recommended.

Note that the strandedness of regions will not be considered when computing overlaps. In other words, both forward and reverse reads will be counted into each region, regardless of the strandedness of that region. This can be altered by setting the forward slot in the param object to only count reads from one strand or the other. The strandedness of the output rowRanges will depend on the strand(s) from which reads were counted.

See windowCounts for more details on read extension.

Value

A RangedSummarizedExperiment object is returned containing one integer matrix. Each entry of the matrix contains the count for each library (column) at each region (row). The coordinates of each region are stored as the rowRanges. The total number of reads, read length and extension length used in each library are stored in the colData. Other parameters (e.g., param) are stored in the metadata.

Author(s)

Aaron Lun

See Also

countOverlaps, windowCounts, readParam

Examples

# A low filter is only used here as the examples have very few reads.
bamFiles <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
incoming <- GRanges(c('chrA', 'chrA', 'chrB', 'chrC'), 
    IRanges(c(1, 500, 100, 1000), c(200, 1000, 700, 1500)))
regionCounts(bamFiles, regions=incoming)
regionCounts(bamFiles, regions=incoming, param=readParam(restrict="chrB"))

# Loading PE data.
bamFile <- system.file("exdata", "pet.bam", package="csaw")
regionCounts(bamFile, regions=incoming, param=readParam(pe="both"))
regionCounts(bamFile, regions=incoming, param=readParam(max.frag=100, 
	pe="first", restrict="chrA"))

LTLA/csaw documentation built on Dec. 11, 2023, 5:11 a.m.