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

Description Usage Arguments Value Examples

View source: R/readData.R

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

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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

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

genomation documentation built on Nov. 1, 2018, 2:12 a.m.