gffReadGR {ballgown} | R Documentation |
(very) light wrapper for rtracklayer::import
gffReadGR(gtf, splitByTranscript = FALSE, identifier = "transcript_id", sep = "; ")
gtf |
name of GTF/GFF file on disk |
splitByTranscript |
if |
identifier |
name of transcript identifier column of |
sep |
field separator in the |
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)