getAlignmentQuality: Calculation of basic alignments statistics

Description

Calculates some basic alignment statistics for given bam files.

Usage

getAlignmentQuality(bamFile, verbose = FALSE, mc.cores = 1)

Arguments

bamFile

A character vector with the filenames of the bam files

verbose

If set to TRUE, some status information is written to the R console.

mc.cores

Number of cores to be used.

Value

Returns a data frame with one row for each given bam file and the columns as listed in the details section.

Details

The given bam files should have marked duplicates and not uniquely mapped reads should have a quality value of 0. In detail, this function returns a data frame with the following columns:

Sample: File name without path and suffix
HeaderID: ID field from bam header, if available
HeaderSampleID: SM field from bam header, if available
HeaderLibraryID: LB field from bam header, if available
TotalReads: Total number of reads in bam file
MappedReads: Number of mapped Reads
MappedReadsRel: MappedReads/TotalReads
UniquelyMappedReads: Number of mapped reads with mapping quality larger 0
UniquelyMappedReadsRel: UniquelyMappedReads/MappedReads
UniquelyMappedUniqueReads: Number of non duplicated mapped reads with mapping quality larger 0
UniquelyMappedUniqueReadsRel: UniquelyMappedUniqueReads/MappedReads
NonRedundantFraction: UniquelyMappedUniqueReads/UniquelyMappedReads
QualMean: Mean mapping quality of all uniquely mapped unique reads
QualSd: Standard deviation of the mapping quality of all uniquely mapped unique reads
Quantile0: 0% quantileof the mapping quality of all uniquely mapped unique reads
Quantile25: 25% quantile of the mapping quality of all uniquely mapped unique reads
Quantile50: 50% quantile of the mapping quality of all uniquely mapped unique reads
Quantile75: 75% quantile of the mapping quality of all uniquely mapped unique reads
Quantile100: 100% quantile of the mapping quality of all uniquely mapped unique reads
Path: Full path and file name as given in argument bamFile

Examples

Run this code

## Not run: getAlignmentQuality("myFile.bam")

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