summarizeAlignment: Summarize alignment results

In jotsetung/SeqUtils: Utility functions for high throughput sequencing

Description

This function summarized the results from an alignment by reading through the corresponding BAM file and counting the number of uniquely aligned or multi-mapped reads.

Usage

summarizeAlignment( x, index=character(), sbp=ScanBamParam( what=c( "flag", "mapq" ), tag=c( "NH", "HI" ) ), yieldSize=1e+6, v=FALSE )

Arguments

x	The file name of the BAM file to summarize.
index	The file name of the index file for the BAM (usually the BAM filename with suffix ".bai").
sbp	The ScanBamParam specifying which fields to read.
yieldSize	The number of entries that should be sequentially processed.
v	verbosity.

Details

This function scans throught the full BAM file and records the number of uniquely or multi-aligned reads along with their mapping quality.

Value

A list with 3 elements:

• flag a list of 3 matrices no_algn, unique_algn and multi_algn with rows corresponding to the BAM flags and (one) column with the number of reads for a certain flag.

• mapq a list of 3 matrices no_algn, unique_algn and multi_algn with 256 rows corresponding to all possible mapping qualities (Sanger Phred encoded; from 0 to 255) and (one) column with the number of reads with a certain map quality.

• counts a list of 3 numeric values no_algn, unique_algn and multi_algn representing the total number of non-, unique- or mult-mapping reads, respectively.

Author(s)

Johannes Rainer

Examples

dirpath <- system.file( package="SeqUtils", "extdata" )
bamfile <- dir( dirpath, "example.bam", full=TRUE )

Res <- summarizeAlignment( bamfile )
Res$counts

jotsetung/SeqUtils documentation built on May 19, 2019, 9:41 p.m.