makeMaskedFasta {AllelicImbalance} | R Documentation |
Replaces all selected positions in a fasta file with the character N
makeMaskedFasta(fastaIn, ...) ## S4 method for signature 'character' makeMaskedFasta(fastaIn, fastaOut, posToReplace, splitOnSeqlevels = TRUE, verbose = TRUE)
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 |
Jesper R. Gadin
data(ASEset.sim) gr <- rowRanges(ASEset.sim) fastaIn <- system.file('extdata/hg19.chr17.subset.fa', package='AllelicImbalance') makeMaskedFasta(fastaIn=fastaIn, fastaOut="fastaOut",posToReplace=gr)