R/recount_genes-data.R

In recount: Explore and download data from the recount project

#' Gene annotation used in recount
#'
#' Gene annotation extracted from Gencode v25 (GRCh38.p7) used in recount.
#' Data extraced on October 12th, 2017. The symbols were updated compared
#' to the version from January 17th, 2017.
#' It includes the sum of the width of the disjoint exons which can be
#' used for normalizing the counts provided in the
#' [RangedSummarizedExperiment-class][SummarizedExperiment::RangedSummarizedExperiment-class] objects.
#'
#' @name recount_genes
#' @docType data
#' @format A [GRanges-class][GenomicRanges::GRanges-class] with one range per gene. The
#' names match their Gencode v25 ids. The [GRanges-class][GenomicRanges::GRanges-class]
#' has three metadata columns.
#' \describe{
#'     \item{gene_id }{  the Gencode v25 ids, identical to the names.}
#'     \item{bp_length }{ the sum of the width of the disjoint exons for that
#'     given gene.}
#'     \item{symbol }{ a CharacterList with the corresponding gene symbols.}
#' }
#' @keywords datasets
#' @seealso [reproduce_ranges], [recount_exons]
#' @references <https://jhubiostatistics.shinyapps.io/recount/>
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