compEpiTools (version 1.6.3)

GR2fasta-methods: A GRanges method to extract and write to the disk a fasta file containing genomic sequences for the GRanges regions in a genome

Description

Given a GRanges and a reference genome returns the sequences for all the ranges as in fasta format.

Methods

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.

Examples

	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))