getAlignmentQuality {epigenomix} | R Documentation

## 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.

### 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`

### Value

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

### Author(s)

Hans-Ulrich Klein (hklein@broadinstitute.org)

### Examples

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

[Package epigenomix version 1.32.0 Index]