getGenes {ballgown} | R Documentation |
label assembled transcripts with gene names
getGenes(gtf, assembled, UCSC = TRUE, attribute = "gene_id")
gtf |
path to a GTF file containing locations of annotated transcripts |
assembled |
GRangesList object, with each set of ranges representing exons of an assembled transcript. |
UCSC |
set to |
attribute |
set to attribute name in |
chromosome labels in gtf
and assembled
should match.
(i.e., you should provide the path to a gtf corrsponding to the same
annotation you used when constructing assembled
)
an IRanges CharacterList
of the same length as
assembled
, providing the name(s) of the gene(s) that overlaps each
transcript in assembled
.
Alyssa Frazee, Andrew Jaffe
data(bg) gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown') geneoverlaps = getGenes(gtfPath, structure(bg)$trans, UCSC=FALSE)