depmap: Cancer Dependency Map Data Package

#' copyNumber_22Q2
#'
#' The `copyNumber` dataset contains the 22Q2 inferred copy number data for
#' genes and cancer cell lines. This dataset includes data from 25368 genes,
#' 1754 cell lines, 35 primary diseases and 38 lineages. The columns of
#' `copyNumber` are: `depmap_id`, a foreign key corresponding to the cancer
#' cell lineage, `cell_line` containing the common CCLE name of the cancer cell
#' lines, `gene` containing both the HUGO gene name of the knockdown gene along
#' with entrez ID#, `gene_name` containing only the HUGO gene name, `entrez_id`
#' containing only the entrez ID#, and `log_copy_number` containing the
#' numerical dependency score values for each pair of genes and cell lines.
#' This dataset can be loaded into the R environment with the
#' `depmap_copyNumber` function.
#'
#' @format A data frame with 44799888 rows (cell lines) and 6 variables.
#'
#' \describe{
#'      \item{depmap_id}{Cancer cell line foreign key (i.e. "ACH-00001")}
#'      \item{gene}{HUGO symbol (e.g. "SAP25") and Entrez ID# (e.g. 100316904)}
#'      \item{gene_name}{HUGO symbol (e.g. "SAP25")}
#'      \item{entrez_id}{Entrez ID# (e.g. 100316904)}
#'      \item{log_copy_number}{numerical log fold change in copy number for a
#'      given gene and cell line}
#'      \item{cell_line}{CCLE name of cancer cell line (i.e. "184A1_BREAST")}
#' }
#'
#' @details This data represents the `CCLE_gene_cn.csv` file taken from the
#' 22Q2 [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 37907473 rows
#' (cell lines) and 6 variables representing 23299 genes, 1604 cell lines, 38
#' primary diseases and 33 lineages.
#'
#' - 19Q2: adds 23 cell lines and 1 lineage
#'
#' - 19Q3: adds 3263 genes, 30 cell lines and removes 2 primary diseases. Now a
#' dataframe with 45670234 rows and 6 variables
#'
#' - 19Q4: adds 77 genes, 25 cell lines, 0 primary diseases and 2 lineages
#'
#' - 20Q1: adds 31 cell lines
#'
#' - 20Q2: adds 32 cell lines
#'
#' - 20Q3: no change
#'
#' - 20Q4: removes 77 genes, adds 8 cell lines and 1 lineage
#'
#' - 21Q1: removes 13 cell lines
#'
#' - 21Q2: adds 2 cell lines
#'
#' - 21Q3: removes 1 cell line and 1 lineage
#'
#' - 21Q4: removes 194 genes and adds 9 cell lines
#'
#' - 22Q1: removes 2000 genes, adds 4 cell lines and 1 lineage
#'
#' - 22Q2: adds 12 cell lines and removes 2 primary diseases and 8 lineages
#'
#' @keywords datasets
#'
#' @examples
#' \dontrun{
#' depmap_copyNumber()
#' }
#'
#' @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.
#'
#' DepMap, Broad (2019): DepMap Achilles 19Q1
#' Public. https://figshare.com/articles/DepMap_Achilles_19Q1_Public/7655150
#'
#' Robin M. Meyers, Jordan G. Bryan, James M. McFarland, Barbara A. Weir, ...
#' David E. Root, William C. Hahn, Aviad Tsherniak. Computational correction of
#' copy number effect improves specificity of CRISPR-Cas9 essentiality screens
#' in cancer cells. Nature Genetics 2017 October 49:1779–1784.
#'
#' 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).
#'
#' @source DepMap, Broad Institute: https://depmap.org/portal/download/
#'
#' @aliases depmap_copyNumber copyNumber_19Q1 copyNumber_19Q2 copyNumber_19Q3
#' copyNumber_19Q4 copyNumber_20Q1 copyNumber_20Q2 copyNumber_20Q3
#' copyNumber_20Q4 copyNumber_21Q1 copyNumber_21Q2 copyNumber_21Q3
#' copyNumber_21Q4 copyNumber_22Q1 copyNumber_22Q2
#'
#' @rdname copyNumber
copyNumber <- NULL