import-bcf: Import Bcf Selection

In AllelicImbalance: Investigates Allele Specific Expression

Description

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

Usage

impBcfGRL(UserDir, ...)

## S4 method for signature 'character'
impBcfGRL(UserDir, searchArea = NULL, verbose = TRUE, ...)

impBcfGR(UserDir, ...)

## S4 method for signature 'character'
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.

Details

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

Value

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

Note

Make sure there is a complementary index file *.bcf.csi for each bcf file in UserDir. If there is not, then the functions impBcfGRL and impBcfGR will try to create them.

Author(s)

Jesper R. Gadin, Lasse Folkersen

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)

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