readsDupFreq {ATACseqQC} | R Documentation

## Calculating duplication frequency

### Description

Calculating the frequency of read duplication based on alignment status determined by rname, strand, pos, cigar, mrnm, mpos and isize.

### Usage

    readsDupFreq(bamFile, index = bamFile)

### Arguments

`bamFile` | A character vector of length 1L containing the name of a BAM file. Only a BAM file with duplication reads are meaningful for estimating the library complexity. For example, a raw BAM file output by aligners, or a BAM file with mitochondrial reads removed.
`index` | A character vector of length 1L containing the name of a BAM index file.

### Value

A two-column matrix of integers. The 1st column is the frequency j = 1,2,3,.... The 2nd column is the number of genomic regions with the same fequency (j) of duplication. The frequency column is in ascending order.

### Author(s)

Haibo Liu

### Examples

    bamFile <- system.file("extdata", "GL1.bam", package = "ATACseqQC")
    freq <- readsDupFreq(bamFile)

[Package ATACseqQC version 1.11.8 Index]