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

tssObjectExample <- cDNAtoBED(gsqFile="gsq.At_GenomicSeq.fasta", fileName="testOut.bed")


[Package TSRchitect version 1.10.0 Index]