gtfToBed: Extract the Chromosomal Information Required in bed Format...

In GeneticTools: Collection of Genetic Data Analysis Tools

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, output="min")

Arguments

gtf	An imported gtf table.
output	Option to format the output, see details.

Details

Currently the function supports only gtf files for human organisms. If applied to other organisms the code has to be changed in such a way that the Chromosome names are adjusted. The output can be formated with the output option, where output="min" results in one row per gene and output="full" keeps the original format in the gtf file.

Value

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

Author(s)

Daniel Fischer

Examples

## Not run: 
annotTrack <- read.table(file="Homo_sapiens.GRCh37.70.gtf",sep="\t")
annotBed <- gtfToBed(annotTrack)

## End(Not run)

GeneticTools documentation built on Jan. 15, 2017, 11:21 a.m.