numReadsInBed {icetea} | R Documentation

## Count the number of reads in a given GRanges

### Description

Count the number of reads in a given GRanges

### Usage

    numReadsInBed(regions, bams = NA, countall = FALSE)

### Arguments

`regions` | The GRanges object to count reads in.
`bams` | character. path to bam files from where the reads have to be counted
`countall` | logical. whether to keep both reads of paired-end data

### Value

Total counts within given ranges per BAM file.

[Package icetea version 1.8.0 Index]