Count reads from a BamFile

Description

Given the tiling of the genome created when the GreyList object was created (or replaced via getKaryotype), count reads overlapping the bins, in preparation for estimating the threshold for grey-listing bins.

Usage

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countReads(obj,bamFile)

Arguments

obj

A GreyList object on which to count reads.

bamFile

A BamFile from which to count reads.

Details

This method counts reads contained within the bins that make up the genome tiling. Bins are overlapping (by default 1Kb bins at 512b intervals) so reads are counted once for each bin that wholly contains them.

Value

The modified GreyList object, with added counts.

Author(s)

Gord Brown

See Also

GreyList, BamFile

Examples

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# Load a pre-built GreyList object.
data(greyList)

path <- system.file("extra", package="GreyListChIP")
## Not run: fn <- file.path(path,"sample_chr21.bam")
## Not run: gl <- countReads(gl,fn)