GR2fasta-methods {compEpiTools} | R Documentation |
Given a GRanges and a reference genome returns the sequences for all the ranges as in fasta format.
To be used in this form:
GR2fasta(GR, org, fastaFile=NULL)
where:
GR: GRanges
org: an object of class BSgenome
fastaFile: character or NULL; an optional file name for the file to be written on disk
For each range in the gr GRanges , the unmasked reference sequenced is retrieved. All the sequences are returned in fasta format, named by the genomic ranges in UCSC format, and optionally written on disk.
require(BSgenome.Mmusculus.UCSC.mm9) gr <- GRanges(Rle(c('chr1','chr2')), ranges=IRanges(start=c(1e7, 2e7), end=c(1e7+19, 2e7+19))) show(GR2fasta(GR=gr, org=Mmusculus, fastaFile=NULL))