getInBuiltAnnotation: Retrieve in-built annotations provided by featureCounts...

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/getInBuiltAnnotation.R

Description

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

Usage

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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

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

Example output

NCBI RefSeq annotation for hg38 (build 38.2).
     GeneID  Chr Start   End Strand
1 100287102 chr1 11874 12227      +
2 100287102 chr1 12613 12721      +
3 100287102 chr1 13221 14409      +
4    653635 chr1 14362 14829      -
5    653635 chr1 14970 15038      -

Rsubread documentation built on Nov. 9, 2018, 6 p.m.