preparePromoterAnnotation: Prepares promoter annotation from a gtf or txdb

Description Usage Arguments Value Examples

View source: R/annotation-data.R

Description

Prepares promoter annotation from a gtf or txdb

Usage

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Arguments

txdb

A txdb object. The txdb of the annotation version for which promoters will be identified. Either 'txdb' or 'file' argument must be specified, but not both.

file

A character object. The file path to a gtf/gff or txdb of the annotation version for which promoters will be identified. Either 'txdb' or 'file' argument must be specified, but not both.

species

A character object. The genus and species of the organism to be used in keepStandardChromosomes(). Supported species can be seen with names(genomeStyles()).

Value

A PromoterAnnotation object. The annotated intron ranges, promoter coordinates and the promoter id mapping are attributes of the promoter annotation data.

Examples

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txdbPath <- system.file('extdata/vignette/annotations/',
                            'gencode.v34.annotation.subset.sqlite', 
                             package = 'proActiv')
txdb <- AnnotationDbi::loadDb(txdbPath)
promoterAnnotation <- preparePromoterAnnotation(txdb = txdb,
                                                species = 'Homo_sapiens')

GoekeLab/proActiv documentation built on June 26, 2021, 6:39 a.m.