txNamesToGeneNames: Convert transcript names to gene names

Description Usage Arguments Value Examples

Description

Works for ensembl, UCSC and other standard annotations.

Usage

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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

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

ORFik documentation built on March 27, 2021, 6 p.m.