countReads-methods: Count reads from a 'BamFile'
In GreyListChIP: Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

Description Usage Arguments Details Value Author(s) See Also Examples

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.

1	countReads(obj,bamFile)

`obj`	A `GreyList` object on which to count reads.
`bamFile`	A `BamFile` from which to count reads.

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.

The modified GreyList object, with added counts.

Gord Brown

GreyList, BamFile

# 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(greyList,fn)