GenomicTools (version 0.2.9.7)

gtfToBed: Extract the Chromosomal Information Required in bed Format from an imported gtf table.

Description

This function creates a matrix of gene annotations in bed format, based on the information given in an importet gtf table.

Usage

gtfToBed(gtf, correctBases=TRUE)

Arguments

gtf

An imported gtf table.

correctBases

Logical subtract 1 from bases

Value

A data.frame in bed format having the four columns Chr, Start, Stop and Gene

Details

After a gtf file was imported with importGTF this function transforms it into a data.frame with bed formatting. The option correctBases adjusts the coordinates in the bed object according to the bed standard. The base counting in gtf starts with 1, wheras in bed-files they start with 0.

Examples

# NOT RUN {
annotTrack <- read.table(file="Homo_sapiens.GRCh37.70.gtf",sep="\t")
annotBed <- gtfToBed(annotTrack)
# }