preparePromoterAnnotation {proActiv} | R Documentation |
Prepares promoter annotation from a gtf or txdb
preparePromoterAnnotation(txdb, file, species)
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()). |
A PromoterAnnotation object. The annotated intron ranges, promoter coordinates and the promoter id mapping are attributes of the promoter annotation data.
txdbPath <- system.file('extdata/vignette/annotations/', 'gencode.v34.annotation.subset.sqlite', package = 'proActiv') txdb <- AnnotationDbi::loadDb(txdbPath) promoterAnnotation <- preparePromoterAnnotation(txdb = txdb, species = 'Homo_sapiens')