buildREmap: Build a genome wide cut site map for a Restriction Enzyme...

In REDseq: Analysis of high-throughput sequencing data processed by restriction enzyme digestion

Description

Build a genome-wide cut map for a Restriction Enzyme (RE)

Usage

buildREmap(REpatternFilePath, format = "fasta", BSgenomeName, outfile)

Arguments

REpatternFilePath	File path storing the recognition pattern of a RE
format	format of the pattern file, either "fasta" (the default) or "fastq
BSgenomeName	BSgenome object, please refer to available.genomes in BSgenome package for details
outfile	temporary output file for writing the matched chromosome location to

Value

Output REmap as a GRanges

Author(s)

Lihua Julie Zhu

Examples

	library(REDseq)
	REpatternFilePath = system.file("extdata", "examplePattern.fa", package="REDseq")
	library(BSgenome.Celegans.UCSC.ce2)
	buildREmap( REpatternFilePath, BSgenomeName=Celegans, outfile=tempfile())

REDseq documentation built on Nov. 8, 2020, 8:19 p.m.