ASEsetFromBam: ASEset from bam file

In AllelicImbalance: Investigates Allele Specific Expression

Description

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

Usage

ASEsetFromBam(gr, ...)

## S4 method for signature 'GRanges'
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.

Author(s)

Jesper R. Gadin

Examples

data(GRvariants)
gr <- GRvariants

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

AllelicImbalance documentation built on Nov. 8, 2020, 6:52 p.m.