groHMM (version 1.6.0)

countMappableReadsInInterval: countMappableReadsInInterval counts the number of mappable reads in a set of genomic features.

Description

Supports parallel processing using mclapply in the 'parallel' package. To change the number of processors, use the argument 'mc.cores'.

Usage

countMappableReadsInInterval(features, UnMap, debug = FALSE, ...)

Arguments

features

A GRanges object representing a set of genomic coordinates. The meta-plot will be centered on the start position.

UnMap

List object representing the position of un-mappable reads. Default: not used.

debug

If set to TRUE, provides additional print options. Default: FALSE

...

Extra argument passed to mclapply

Value

Returns a vector of counts, each representing the number of reads inside each genomic interval.