makeMaskedFasta: makes masked fasta reference

In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

Description

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

Usage

makeMaskedFasta(fastaIn, ...)

## S4 method for signature 'character'
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

Author(s)

Jesper R. Gadin

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)

pappewaio/AllelicImbalance documentation built on April 11, 2020, 2:58 a.m.