depmap: Cancer Dependency Map Data Package

#' RPPA_19Q3
#'
#' The `RPPA` dataset contains the 19Q3 CCLE Reverse Phase Protein Array (RPPA)
#' cellular model expression data. This dataset includes data from 214 genes,
#' 899 cancer cell lines, 28 primary diseases and 28 lineages. The columns of
#' `RPPA` are: `depmap_id`, a foreign key corresponding to the cancer cell
#' lineage, `cell_line` which contains the common CCLE name of the cancer cell
#' lines, `gene` which contains the knockdown gene expression, `antibody`
#' containing the name of knocked down gene and `expression` containing
#' numerical protein expression data. This dataset can be loaded into R
#' environment with the `depmap_RPPA` function.
#'
#' @format A data frame with 192386 rows and 4 variables:
#' \describe{
#'     \item{depmap_id}{cancer cell line foreign key (i.e. "ACH-000001")}
#'     \item{cell_line}{CCLE name of cancer cell line (i.e. "NIHOVCAR3_OVARY")}
#'     \item{antibody}{Name of antibody targeting protein (i.e. "14-3-3_beta")}
#'     \item{expression}{Observed expression via RPPA of protein coding genes}
#' }
#'
#' @details This data represents the `CCLE_RPPA_20181003.csv` file taken from
#' the 19Q3 [Broad Institute](https://depmap.org/portal/download/) cancer
#' depenedency study. The derived dataset found in the `depmap` package features
#' the addition of a foreign key `depmap_id` found in the first column of this
#' dataset, which was added from the `metadata` dataset. This dataset has been
#' converted to a long format tibble. Variables names from the original dataset
#' were converted to lower case, put in snake case, and abbreviated where
#' feasible.
#'
#' @section Change log:
#'
#' - 19Q1: Initial dataset consisted of a data frame with 192386 rows and 4
#' variables representing 214 genes, 899 cancer cell lines, 28 primary diseases
#' and 28 lineages.
#'
#' - 19Q2: no change
#'
#' - 19Q3: no change, no further releases are scheduled at this time.
#'
#' - 19Q4: no change, no further releases are scheduled at this time.
#'
#' - 20Q1: no change, no further releases are scheduled at this time.
#'
#' - 20Q2: no change, no further releases are scheduled at this time.
#'
#' - 20Q3: no change, no further releases are scheduled at this time.
#'
#' - 20Q4: no change, no further releases are scheduled at this time.
#'
#' - 21Q1: no change, no further releases are scheduled at this time.
#'
#' - 21Q2: no change, no further releases are scheduled at this time.
#'
#' - 21Q3: no change, no further releases are scheduled at this time.
#'
#' - 21Q4: no change, no further releases are scheduled at this time.
#'
#' - 22Q1: no change, no further releases are scheduled at this time.
#'
#' - 22Q2: no change, no further releases are scheduled at this time.
#'
#' @docType data
#'
#' @import dplyr
#'
#' @keywords datasets
#'
#' @examples
#' \dontrun{
#' depmap_RPPA()
#' }
#'
#' @references Tsherniak, A., Vazquez, F., Montgomery, P. G., Weir, B. A.,
#' Kryukov, G., Cowley, G. S., ... & Meyers, R. M. (2017). Defining a cancer
#' dependency map. Cell, 170(3), 564-576.
#'
#' Mahmoud Ghandi, Franklin W. Huang, Judit Jané-Valbuena, Gregory V. Kryukov,
#' ... Todd R. Golub, Levi A. Garraway & William R. Sellers. 2019. Next-
#' generation characterization of the Cancer Cell Line Encyclopedia. Nature 569,
#' 503–508 (2019).
#'
#' Haoxin Li, Shaoyang Ning, Mahmoud Ghandi, Gregory V. Kryukov, Shuba Gopal,
#' ... Levi A. Garraway & William R. Sellers. The landscape of cancer cell line
#' metabolism. Nature Medicine 25, 850-860 (2019).
#'
#' @source DepMap, Broad Institute: https://depmap.org/portal/download/
#'
#' @rdname RPPA
#'
#' @aliases RPPA_19Q3 RPPA_19Q2 RPPA_19Q1 depmap_RPPA
RPPA <- NULL