ballgown (version 2.4.2)

gffRead: read in GTF/GFF file as a data frame

Description

read in GTF/GFF file as a data frame

Usage

gffRead(gffFile, nrows = -1, verbose = FALSE)

Arguments

gffFile

name of GTF/GFF on disk

nrows

number of rows to read in (default -1, which means read all rows)

verbose

if TRUE, print status info at beginning and end of file read. Default FALSE.

Value

data frame representing the GTF/GFF file

See Also

getAttributeField to extract data from "attributes" column; http://useast.ensembl.org/info/website/upload/gff.html for more information on the GTF/GFF file format.

Examples

gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')
annot = gffRead(gtfPath)