alignmentStats {QuasR} | R Documentation

## Get statistics on alignments

### Description

Get statistics on alignments from bam file or `qProjec` object.

### Usage

    alignmentStats(x, collapseBySample=TRUE)

### Arguments

`x` | the source of alignment bam files, one of: a `character` vector with bam files a `qProject` object
`collapseBySample` | If `TRUE` and `x` is a `qProject` object, sum counts for bam files with identical sample names.

### Details

Internally, `alignmentStats` queries the bam index files similar to 'idxstats' from samtools. Please note that this does not discriminate for example between primary and secondary alignments. If you need more statistics, see for example `quickBamFlagSummary` from package Rsamtools.

If `x` is a `qProject` object, the auxiliary bam files will not contain any unmapped reads, and the corresponding unmapped counts are calculated by subtracting auxiliary mapped counts from the total reads. The latter correspond to the unmapped counts from the corresponding genome bam files.

### Value

A `matrix` with one row per bam file and three columns ("seqlength", "mapped" and "unmapped").

### Author(s)

Anita Lerch, Dimos Gaidatzis and Michael Stadler

### See Also

`qProject`, `quickBamFlagSummary` from package Rsamtools

### Examples

    ## Not run:
        # see qProject manual page for an example
        example(qProject)

    ## End(Not run)

[Package QuasR version 1.28.0 Index]