getInBuiltAnnotation {Rsubread}R Documentation

Retrieve In-Built Annotations

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.

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.

Value

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

Author(s)

Wei Shi

See Also

featureCounts

Examples

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

[Package Rsubread version 2.6.4 Index]