writeHits {REDseq} | R Documentation |
write the hits of pattern search to a bed file, internal function used by searchPattern
writeHits(seqname, matches, strand, file = "", append = FALSE)
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 |
results are saved in the file specified by outfile
Lihua Julie Zhu
http://bioconductor.org/packages/2.8/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf
searchPattern, buildREmap
library(REDseq) x <- DNAString("AAGCGCGATATG") m <- matchPattern("GCGC", x) REDseq:::writeHits(seqname="chr1", m, strand="+",file="exampleWriteHits.bed", append=FALSE)