promoterRegions {Rsubread}R Documentation

Generate Annotation for Promoter Region of Genes

Description

Create an SAF data-frame of genewise promoter regions.

Usage

promoterRegions(

    annotation = "mm10",
    upstream = 3000L,
    downstream = 2000L)

Arguments

annotation

a character string giving the name of a genome with built-in annotation or an SAF format gene annotation. If using built-in annotation, the character string should be one of the following: mm10, mm9, hg38 or hg19. They correspond to the NCBI RefSeq annotations for genomes ‘mm10’, ‘mm9’, ‘hg38’ and ‘hg19’, respectively. mm10 by default.

upstream

an integer giving the number of upstream bases that will be inclued in the promoter region generated for each gene. These bases are taken immediately upstream (5' end) from transcriptional start site of each gene.

downstream

an integer giving the number of downstream bases that will be inclued in the promoter region generated for each gene. These bases are taken immediately downstream (3' end) from transcriptional start site of each gene.

Details

This function takes as input an SAF format gene annotation and produces an SAF format annotation that contains chromosomal coordinates of promoter region of each gene. See featureCounts for definition of the SAF format.

Built-in annotations can be accessed via function getInBuiltAnnotation.

Value

An SAF format data.frame with columns GeneID, Chr, Start, End and Strand.

Author(s)

Gordon K Smyth

See Also

featureCounts, getInBuiltAnnotation

Examples

x <- promoterRegions()
head(x)

[Package Rsubread version 2.2.6 Index]