countAllelesFromBam {AllelicImbalance} | R Documentation |
count alleles before creating ASEse.
countAllelesFromBam(gr, ...) ## S4 method for signature 'GRanges' countAllelesFromBam( gr, pathToDir, flag = NULL, scanBamFlag = NULL, return.class = "array", verbose = TRUE, ... )
gr |
GRanges that contains SNPs of interest |
... |
arguments to pass on |
pathToDir |
path to directory of bam files |
flag |
specify one flag to use as filter, default is no filtering. allowed flags are 99, 147, 83 and 163 |
scanBamFlag |
set a custom flag to use as filter |
return.class |
type of class for the returned object |
verbose |
makes funciton more talkative |
counts the alleles in a bam file based on GRanges positions.
Important excerpt from the details section of the internal applyPileups function: Regardless of 'param' values, the algorithm follows samtools by excluding reads flagged as unmapped, secondary, duplicate, or failing quality control.
Jesper R. Gadin
data(GRvariants) gr <- GRvariants ##not run at the moment #pathToDir <- system.file('inst/extdata/ERP000101_subset', package='AllelicImbalance') #ar <- countAllelesFromBam(gr, pathToDir)