cDNAtoBED {TSRchitect} | R Documentation |
cDNAtoBED
converts aligned cDNA data (in .gsq format)
to BED format, extracting the 5'-most base.
cDNAtoBED(gsqFile, fileName = "gsqOut.bed") ## S4 method for signature 'character,character' cDNAtoBED(gsqFile, fileName = "gsqOut.bed")
gsqFile |
a path to the gsq (GeneSeqer) output file (class character) |
fileName |
the name (class character) of the BED file to be written (default is "gsqOut.bed") |
a BED file containing a list of the 5'-most base from each of the alignments contained in the GeneSeqer (.gsq) output file is written to the user's working directory.
extdata.dir <- system.file("extdata", package="TSRchitect") tssObjectExample <- cDNAtoBED(gsqFile=paste(extdata.dir,"AtEST.gsq",sep="/"), fileName="testOut.bed")