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]