gffReadGR: read in gtf file as GRanges object
In alyssafrazee/ballgown: Flexible, isoform-level differential expression analysis

Description Usage Arguments Value Author(s) See Also Examples

(very) light wrapper for rtracklayer::import

gffReadGR(
  gtf,
  splitByTranscript = FALSE,
  identifier = "transcript_id",
  sep = "; "
)

`gtf`	name of GTF/GFF file on disk
`splitByTranscript`	if `TRUE`, return a `GRangesList` of transcripts; otherwise return a `GRanges` object containing all genomic features in `gtf`. Default `FALSE`.
`identifier`	name of transcript identifier column of `attributes` field in `gtf`. Default `"transcript_id"`. Only used if `splitByTranscript` is `TRUE`.
`sep`	field separator in the `attributes` field of `gtf`. Default `"; "` (semicolon + space). Only used if `splitByTranscript` is `TRUE`.

if splitByTranscript is FALSE, an object of class GRanges representing the genomic features in gtf. If splitByTranscript is TRUE, an object of class GRangesList, where each element is a GRanges object corresponding to an annotated transcript (designated in names).

Alyssa Frazee

gffRead for reading in a GTF file as a data frame rather than a GRanges/GRangesList object.

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

# read in exons as GRanges:
annotgr = gffReadGR(gtfPath)

# read in groups of exons as transcripts, in GRangesList:
transcripts_grl = gffReadGR(gtfPath, splitByTranscript=TRUE)