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)
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