txNamesToGeneNames {ORFik}

R Documentation

Convert transcript names to gene names

Description

Works for ensembl, UCSC and other standard annotations.

Usage

txNamesToGeneNames(txNames, txdb)

Arguments

txNames	character vector, the transcript names to convert. Can also be a named object with tx names (like a GRangesList), will then extract names.
txdb	the transcript database to use or gtf/gff path to it.

Value

character vector of gene names

Examples

gtf <- system.file("extdata/Danio_rerio_sample", "annotations.gtf", package = "ORFik")
txdb <- loadTxdb(gtf)
loadRegions(txdb, "cds") # using tx names
txNamesToGeneNames(cds, txdb)
# Identical to:
loadRegions(txdb, "cds", by = "gene")

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