bam2counts: Compute the number of reads fall into specific genomic region
In intePareto: Integrative Analysis of RNA-Seq and ChIP-Seq Data

Description Usage Arguments Value Examples

bam2counts computes the number of reads fall into specific genomic region such as promoter, enhancer, genebody

1	bam2counts(bamFile, region, fragLength = 180)

`bamFile`	Aligned bam file as input.
`region`	The GRanges object defined by user to calculate the number of reads fall into this specific region. For ChIP-Seq of histone modifications they are usually promoter, enhancer and genebody regions.
`fragLength`	Extend reads toward the 3'-end to the average DNA fragment size obtained after DNA size selection

a vector of numbers

1
2
3

data("promoter")
file.bam <- system.file("extdata", "SRR925640.bam", package = "intePareto")
bam2counts(bamFile = file.bam, region = promoter, fragLength = 180)