wavClusteR (version 2.6.2)

getAllSub: Identify all substitutions observed across genomic positions exhibiting a specified minimum coverage

Description

All substitutions observed across genomic positions exhibiting user-defined minimum coverage are extracted and a count table is returned. This function supports parallel computing.

Usage

getAllSub(sortedBam, minCov = 20, cores = 1)

Arguments

sortedBam

GRanges object containing aligned reads as returned by readSortedBam

minCov

An integer defining the minimum coverage required at a genomic position exhibiting a substitution. Genomic positions of coverage less than minCov are discarded. Default is 20 (see Details).

cores

An integer defining the number of cores to be used for parallel processing, if available. Default is 1.

Value

• A GRanges object containing a count table, where each range correspond to a substitution. The metadata correspond to the following information:
• substitutions
  observed substitution, e.g. AT, i.e. A in the reference sequence and T in the mapped read.
• coverage
  strand-specific coverage.
• count
  number of strand-specific substitutions.

Details

The choice of the minimum coverage influences the variance of the relative substitution frequency estimates, which in turn affect the mixture model fit. A conservative value depending on the library size is recommended for a first analysis. Values smaller than 10 have not been tested and are therefore not recommended.

See Also

readSortedBam

Examples

filename <- system.file( "extdata", "example.bam", package = "wavClusteR" )
example <- readSortedBam(filename = filename)
countTable <- getAllSub( example, minCov = 10, cores = 1 )
countTable