Rsubread (version 1.22.2)

getInBuiltAnnotation: Retrieve in-built annotations provided by featureCounts function

Description

Retrieve an in-built annotation and save it to a data frame

Usage

getInBuiltAnnotation(annotation="mm10")

Arguments

annotation

a character string specifying the in-built annotation to be retrieved. It has four possible values including mm10, mm9, hg38 and hg19, corresponding to the NCBI RefSeq annotations for genomes `mm10', `mm9', `hg38' and `hg19', respectively. mm10 by default.

Value

A data frame with five columns including GeneID, Chr, Start, End and Strand.

Details

The featureCounts read summarization function provides in-built annotations for conveniently summarizing reads to genes or exons, and this function allows users to have access to those in-built annotations.

For more information about these annotations, please refer to the help page for featureCounts function.

See Also

featureCounts

Examples

library(Rsubread)
x <- getInBuiltAnnotation("hg38")
x[1:5,]