depmap: Cancer Dependency Map Data Package

#' mutationCalls_22Q2
#'
#' The `mutationCalls` dataset contains merged the 22Q2 mutation calls (for
#' coding region, germline filtered) and includes data from 18784 genes, 1771
#' cell lines, 33 primary diseases and 30 lineages. This dataset can be
#' considered the metadata data set for mutations and does not contain any
#' dependency data. This dataset can be loaded into the R environment with the
#' `depmap_mutationCalls` function.
#'
#'
#' @format A data frame with 1235466 rows and 32 variables:
#' \describe{
#'   \item{depmap_id}{depmap_id}
#'   \item{gene_name}{Hugo Symbol denotes a unique and meaningful name for each
#'   gene (e.g. SAP25)}
#'   \item{entrez_id}{Gene ID for NCBI Entrez gene database, (e.g. 100316904)}
#'   \item{ncbi_build}{NCBI Build (i.e. reference genome)}
#'   \item{chromosome}{Chromosome}
#'   \item{start_pos}{Gene start position}
#'   \item{end_pos}{Gene end position}
#'   \item{strand}{Strand location of gene}
#'   \item{var_class}{Variant Classification}
#'   \item{var_type}{Variant Type}
#'   \item{ref_allele}{Reference Allele}
#'   \item{alt_allele}{Tumor Seq Allele1}
#'   \item{dbSNP_RS}{Single Nucleotide Polymorphism Database (dbSNP) reference
#'    cluster}
#'   \item{dbSNP_val_status}{dbSNP Val Status}
#'   \item{genome_change}{Genome Change}
#'   \item{annotation_transcript}{Annotation Transcript}
#'   \item{cDNA_change}{change in cDNA}
#'   \item{codon_change}{Codon_Change}
#'   \item{protein_change}{Protein_Change}
#'   \item{is_deleterious}{Status of gene knockout on cell lineage}
#'   \item{is_tcga_hotspot}{isTCGAhotspot}
#'   \item{tcga_hsCnt}{TCGAhsCnt}
#'   \item{is_cosmic_hotspot}{isCOSMIChotspot}
#'   \item{cosmic_hsCnt}{COSMIChsCnt}
#'   \item{ExAC_AF}{ExAC_AF}
#'   \item{CGA_WES_AC}{CGA_WES_AC}
#'   \item{sanger_WES_AC}{SangerWES_AC}
#'   \item{RNAseq_AC}{RNAseq_AC}
#'   \item{HC_AC}{HC_AC}
#'   \item{RD_AC}{RD_AC}
#'   \item{WGS_AC}{WGS_AC}
#'   \item{var_annotation}{Variant_annotation}
#' }
#'
#' @details This data represents the `CCLE_mutations.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 for package consisted of dataframe with
#'   1243145 rows and 35 variables representing 18755 genes, 1601 cell
#'   lines, 37 primary diseases and 33 lineages.
#'
#' - 19Q2: adds 30 cell lines, 1 primary disease and 1 lineage. This
#'   version has different columns than the previous version: the
#'   variable "VA_WES_AC" is no longer present in this dataset. Some
#'   minor alterations to the original file were made. The first
#'   column of the original dataset, (ID, Sample number) was removed,
#'   as this column was only the row number and did not serve any
#'   unique identifying purpose.
#'
#' - 19Q3: adds 1 gene, 25 cell lines and removes 1 primary disease.
#'
#' - 19Q4: adds 1 gene, 10 cell lines, 0 primary diseases and 2
#'   lineages.
#'
#' - 20Q1: adds 4 genes, 31 cell lines, 1 lineage.
#'
#' - 20Q2: adds 44 cell lines, 1 lineage.
#'
#' - 20Q3: no change.
#'
#' - 20Q4: removes 13 genes, adds 8 cell lines and 1 lineage. Columns
#'  `tumor_sample_barcode` and `sanger_recalib_WES_AC` were removed.
#'
#' - 21Q1: removes 11 genes and 2 cell lines.
#'
#' - 21Q2: removes 1 genes and adds 3 cell lines.
#'
#' - 21Q3: removes 3 genes, 4 cell lines and 1 lineage.
#'
#' - 21Q3: removes 3 genes, 4 cell lines and 1 lineage.
#'
#' - 21Q4: adds 9 cell lines.
#'
#' - 22Q1: adds 4 cell lines and 1 lineage. The variable `tumor_seq_allele1`
#'   was renamed `alt_allele`.
#'
#' - 22Q2: adds 12 cell lines and removes 2 primary diseases and 8
#'   lineages.
#'
#' @docType data
#'
#' @import dplyr
#'
#' @keywords datasets
#'
#' @examples
#' \dontrun{
#' depmap_mutationCalls()
#' }
#'
#' @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/
#'
#' @rdname mutationCalls
#'
#' @aliases depmap_mutationCalls mutationCalls_19Q1  mutationCalls_19Q2
#' mutationCalls_19Q3 mutationCalls_19Q4 mutationCalls_20Q1 mutationCalls_20Q2
#' mutationCalls_20Q3 mutationCalls_20Q4 mutationCalls_21Q1 mutationCalls_21Q2
#' mutationCalls_21Q3 mutationCalls_21Q4 mutationCalls_22Q1 mutationCalls_22Q2
#'
mutationCalls <- NULL