get gene names from a ballgown object
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a ballgown object
This vector differs from that produced by geneIDs in that geneNames produces
*annotated* gene names that correspond to assembled transcripts. The
return will be empty/blank/NA if the transcriptome assembly is de novo
(i.e., was not compared to an annotation before the ballgown object was
getGenes for matching transcripts to gene names.
Some entries of this vector will be empty/blank/NA if the corresponding
transcript did not overlap any annotated genes.
named vector of gene names included in the ballgown object, named and ordered by corresponding numeric transcript ID.
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data(bg) # this is a de novo assembly, so it does not contain gene info as it stands # but we can add it: annot = system.file('extdata', 'annot.gtf.gz', package='ballgown') gnames = getGenes(annot, structure(bg)$trans, UCSC=FALSE) gnames_first = lapply(gnames, function(x) x) #just take 1 overlapping gene expr(bg)$trans$gene_name = gnames_first # now we can extract these gene names: geneNames(bg)
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