getGenes: label assembled transcripts with gene names

In ballgown: Flexible, isoform-level differential expression analysis

Description

label assembled transcripts with gene names

Usage

getGenes(gtf, assembled, UCSC = TRUE, attribute = "gene_id")

Arguments

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 TRUE if you're using a UCSC gtf file. (Requires some extra text processing).
attribute	set to attribute name in gtf that gives desired gene identifiers. Default "gene_id"; another commone one is "gene_name" (for the gene symbol).

Details

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)

Value

an IRanges CharacterList of the same length as assembled, providing the name(s) of the gene(s) that overlaps each transcript in assembled.

Author(s)

Alyssa Frazee, Andrew Jaffe

Examples

data(bg)
gtfPath = system.file('extdata', 'annot.gtf.gz', package='ballgown')
geneoverlaps = getGenes(gtfPath, structure(bg)$trans, UCSC=FALSE)

ballgown documentation built on Nov. 8, 2020, 5:46 p.m.