R/gencode_annotated_genes.R

In LieberInstitute/GenomicState: Build and access GenomicState objects for use with derfinder tools from sources like Gencode

#' Annotation the genes for a given Gencode TxDb object
#'
#' Based on a `TxDb` object built by [gencode_txdb()] this function annotates
#' the genes. This information is then used by packages like `derfinder` and
#' `derfinderPlot`.
#'
#' @param txdb A [GenomicFeatures::TxDb-class] object built with
#' [gencode_txdb()].
#'
#' @return The annotated genes resulting from
#' [bumphunter::annotateTranscripts()].
#' @export
#' @author Leonardo Collado-Torres.
#' @references Based on code for the `brainflowprobes` package at:
#' <https://github.com/LieberInstitute/brainflowprobes/blob/devel/data-raw/create_sysdata.R>
#'
#' @seealso [gencode_txdb()] [gencode_genomic_state()]
#'
#' @examples
#'
#' ## Start from scratch if you want:
#' \dontrun{
#' txdb_v31_hg19_chr21 <- gencode_txdb("31", "hg19", chrs = "chr21")
#' }
#'
#' ## or read in the txdb object for hg19 chr21 from this package
#' txdb_v31_hg19_chr21 <- AnnotationDbi::loadDb(
#'     system.file("extdata", "txdb_v31_hg19_chr21.sqlite",
#'         package = "GenomicState"
#'     )
#' )
#'
#' ## Obtain the annotated genes for the Gencode TxDb object
#' genes_v31_hg19_chr21 <- gencode_annotated_genes(txdb_v31_hg19_chr21)
#'
#' ## Explore the result
#' genes_v31_hg19_chr21
gencode_annotated_genes <- function(txdb) {
    message(paste(Sys.time(), "annotating the transcripts"))
    genes <- bumphunter::annotateTranscripts(txdb,
        by = "gene",
        mappingInfo = list(
            "column" = "ENTREZID", "keytype" = "ENSEMBL",
            "multiVals" = "first"
        ),
        simplifyGeneID = TRUE
    )
    return(genes)
}