gffToGRanges: Converts a gff formated data.frame into a GenomicRanges...

In BIMSBbioinfo/genomation: Summary, annotation and visualization of genomic data

Description

Converts a gff formated data.frame into a GenomicRanges object. The GenomicRanges object needs to be properly formated for the function to work.

Usage

gffToGRanges(gff.file, filter = NULL, zero.based = FALSE, ensembl = FALSE)

Arguments

gff.file	path to a gff formatted file. The file can end in .gz, .bz2, .xz, or .zip and/or start with http:// or ftp://. If the file is not compressed it can also start with https:// or ftps://.
filter	a character designating which elements to retain from the gff file (e.g. exon, CDS, ...)
zero.based	boolean whether the coordinates are 0 or 1 based. 0 is the default
ensembl	boolean if TRUE, add the chr prefix to seqlevels. FALSE by default

Value

returns a GenomicRanges object

Examples

gff.file = system.file('extdata/chr21.refseq.hg19.gtf', package='genomation')
gff = gffToGRanges(gff.file)

BIMSBbioinfo/genomation documentation built on March 13, 2020, 5:28 a.m.