AllelicImbalance (version 1.10.2)

ASEsetFromBam: ASEset from bam file

Description

count alleles and create an ASEset direct from bam file instead of reading into R first.

Usage

ASEsetFromBam(gr, ...)
"ASEsetFromBam"(gr, pathToDir, PE = TRUE, flagsMinusStrand = c(83, 163), flagsPlusStrand = c(99, 147), strandUnknown = FALSE, ...)

Arguments

gr

GenomicRanges of SNPs to create ASEset for

...

passed on to ASEsetFromBam function

pathToDir

Directory of bam files with index in same directory

PE

if paired end or not (default: TRUE)

flagsMinusStrand

flags that mark reads coming from minus strand

flagsPlusStrand

flags that mark reads coming from plus strand

strandUnknown

default: FALSE

Details

counts the alleles in a bam file based on GRanges positions.

Examples

data(GRvariants)
gr <- GRvariants

##no execution at the moment
#pathToDir <- system.file('inst/extdata/ERP000101_subset', package='AllelicImbalance')
#a <- ASEsetFromBam(gr, pathToDir)