R/data.R

In rChEA3: R Client for the 'ChEA3' Transcription Factor Enrichment API

#' A549 Downregulated Genes (Dex)
#'
#' Example gene set of downregulated (repressed) genes in A549 cells after
#' dexamethasone treatment. To keep the dataset small and suitable for examples
#' and tests, only the first 15 downregulated gene symbols are included here.
#'
#' @format A character vector of length 15, containing HGNC gene symbols.
#'
#' @details
#' The full list of differentially expressed genes (activated and repressed) is
#' provided as Supplementary Table S3 in Tav *et al.* (2023). The raw Excel
#' file can be downloaded directly from *Frontiers in Genetics*:
#' \url{https://www.frontiersin.org/api/v4/articles/1237092/file/Table_3.XLSX/1237092_supplementary-materials_tables_3_xlsx/1}.
#'
#' In this package, we subset the data to only the first 15 repressed genes,
#' which are stored in the object \code{a549_dex_downreg}.
#'
#' @source Supplementary Table S3 from Tav *et al.* (2023).
#'
#' @references
#' Tav C, Fournier É, Fournier M, Khadangi F, Baguette A, Côté MC, Silveira MAD,
#' Bérubé-Simard F-A, Bourque G, Droit A, Bilodeau S (2023).
#' "Glucocorticoid stimulation induces regionalized gene responses within
#' topologically associating domains." \emph{Frontiers in Genetics}.
#' \doi{10.3389/fgene.2023.1237092}
#'
#' @examples
#' # Load dataset
#' data(a549_dex_downreg)
#' a549_dex_downreg
"a549_dex_downreg"