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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/gffRead.R

Description

read in GTF/GFF file as a data frame

Usage

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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

Author(s)

Kasper Hansen

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

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

ballgown documentation built on Nov. 17, 2017, 9:30 a.m.