makeMaskedFasta {AllelicImbalance} | R Documentation

## makes masked fasta reference

### 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)

[Package AllelicImbalance version 1.22.0 Index]