searchPattern {REDseq} | R Documentation |
internal function for searching pattern(s) in a genome used by buildREmap leveraging BSgenome package
searchPattern(dict0, BSgenomeName, outfile = "")
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 |
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
buildREmap
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())