cDNAtoBED {TSRchitect}R Documentation

cDNAtoBED

Description

cDNAtoBED converts aligned cDNA data (in .gsq format) to BED format, extracting the 5'-most base.

Usage

cDNAtoBED(gsqFile, fileName = "gsqOut.bed")

## S4 method for signature 'character,character'
cDNAtoBED(gsqFile,
  fileName = "gsqOut.bed")

Arguments

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")

Value

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.

Examples

extdata.dir <- system.file("extdata", package="TSRchitect")
tssObjectExample <- cDNAtoBED(gsqFile=paste(extdata.dir,"AtEST.gsq",sep="/"),
                              fileName="testOut.bed")

[Package TSRchitect version 1.8.9 Index]