gsq2bed-methods: *gsq2bed*

In TSRchitect: Promoter identification from large-scale TSS profiling data

Description

gsq2bed converts aligned cDNA data (in .gsq format) to BED format, extracting the 5'-most base.

Usage

gsq2bed(gsqFile, outfile)

## S4 method for signature 'character,character'
gsq2bed(gsqFile, outfile)

Arguments

gsqFile	a path to the gsq (GeneSeqer) output file (class character)
outfile	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 <- gsq2bed(gsqFile=paste(extdata.dir,"AtEST.gsq",sep="/"),
                            outfile="")

TSRchitect documentation built on Nov. 8, 2020, 8:11 p.m.