getTranscript2Gene: Gets gene names from annotation

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Gets gene names from annotation

Description

Gets gene names from an annotation data.frame of gtf or gff format.

Usage

getTranscript2Gene(gtf)

countIsoformsPerGene(tr2Gene)

Arguments

gtf	the annotation data.frame to get the gene data from.
tr2Gene	a character vector containing the transcript ID's obtained from the gene ID's.

Value

Returns a character vector with the gene names.

Functions

• countIsoformsPerGene: Returns a contingency table of the transcript names counting isoforms per gene.

Author(s)

Rehrauer, Hubert

Schmid, Peter

Examples

param = ezParam()
gtf = ezLoadFeatures(param, system.file("extdata/genes.gtf", package="ezRun", mustWork=TRUE))
tr2Gene = getTranscript2Gene(gtf)
ipg = countIsoformsPerGene(tr2Gene)

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.