AllelicImbalance (version 1.6.2)

makeMaskedFasta: makes masked fasta reference

Description

Replaces all selected positions in a fasta file with the character N

Usage

makeMaskedFasta(fastaIn, ...)
"makeMaskedFasta"(fastaIn, fastaOut, posToReplace, splitOnSeqlevels = TRUE, verbose = TRUE)

Arguments

fastaIn

character string of the path for the fasta file to be used

...

arguments to pass on

fastaOut

character string of the path for the masked fasta file (no extension)

posToReplace

GRanges object with the genomic ranges to replace

splitOnSeqlevels

write on file for each seqlevel to save memory

verbose

makes function more talkative

Examples

data(ASEset.sim)
gr <- rowRanges(ASEset.sim)
fastaIn <- system.file('extdata/hg19.chr17.subset.fa', package='AllelicImbalance')
makeMaskedFasta(fastaIn=fastaIn, fastaOut="fastaOut",posToReplace=gr)