intePareto (version 0.0.1)

bam2rpm: Compute the normalized number of reads (rpm) fall into specific genomic region

Description

bam2rpm computes the normalized number of reads (rpm) fall into specific genomic region such as promoter, enhancer, genebody

Usage

bam2rpm(bamFile, region, fragLength = 180)

Arguments

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

Value

a vector of numbers

Examples

Run this code
# NOT RUN {
data("promoter")
file.bam <- system.file("extdata", "SRR925640.bam", package = "intePareto")
bam2rpm(bamFile = file.bam, region = promoter, fragLength = 180)
# }

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