AllelicImbalance (version 1.10.2)

import-bcf: Import Bcf Selection

Description

Imports a selection of a bcf file or files specified by a GenomicRanges object as search area.

Usage

impBcfGRL(UserDir, ...)
"impBcfGRL"(UserDir, searchArea = NULL, verbose = TRUE, ...)
impBcfGR(UserDir, ...)
"impBcfGR"(UserDir, searchArea = NULL, verbose = TRUE, ...)

Arguments

UserDir

The relative or full path of folder containing bam files.

...

parameters to pass on

searchArea

A GenomicRanges object that contains the regions of interest

verbose

Setting verbose=TRUE gives details of the procedure during function run.

Value

BcfImpGRList returns a GRangesList object. BcfImpGR returns one GRanges object of all unique entries from one or more bcf files.

Details

A wrapper to import bcf files into R in the form of GenomicRanges objects.

See Also

• The impBamGRL for importing bam files
• The getAlleleCounts for how to get allele(SNP) counts
• The scanForHeterozygotes for how to find possible heterozygote positions

Examples

#Declare searchArea
searchArea <- GRanges(seqnames=c('17'), ranges=IRanges(79478301,79478361))

#Relative or full path  
pathToFiles <- system.file('extdata/ERP000101_subset', package='AllelicImbalance')

#import
reads <- impBcfGRL(pathToFiles, searchArea, verbose=FALSE)