writeHits: write the hits of pattern search to a bed file

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

Description

write the hits of pattern search to a bed file, internal function used by searchPattern

Usage

writeHits(seqname, matches, strand, file = "", append = FALSE)

Arguments

seqname	Chromosome name
matches	XStringViews object storing matched chromosome locations
strand	strand of the match
file	file path where the hits is written to
append	TRUE if append to existing file, false if start a new 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

searchPattern, buildREmap

Examples

	library(REDseq)
	x <- DNAString("AAGCGCGATATG")
	m <- matchPattern("GCGC", x)
	REDseq:::writeHits(seqname="chr1", m, strand="+",file="exampleWriteHits.bed", append=FALSE)

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