searchPattern: search pattern(s) in a genome

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

Description

internal function for searching pattern(s) in a genome used by buildREmap leveraging BSgenome package

Usage

searchPattern(dict0, BSgenomeName, outfile = "")

Arguments

dict0	DNAStringSet object, see examples
BSgenomeName	BSgenome object, please refer to available.genomes in BSgenome package for details
outfile	The file path to write the search results as a bed file

Value

results are saved in the file specified by outfile

Author(s)

Lihua Julie Zhu

References

http://bioconductor.org/packages/2.8/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf

See Also

buildREmap

Examples

	library(REDseq)
	patternFile = system.file("extdata", "examplePattern.fa", package="REDseq")
	example.dict0 <- readDNAStringSet(patternFile, "fasta")
	library(BSgenome.Celegans.UCSC.ce2)
	REDseq:::searchPattern(dict0 = example.dict0, BSgenomeName=Celegans, outfile=tempfile())

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