[GDR-3410] Add public data from DepMap Portal

.gitignore

@@ -40,6 +40,7 @@ vignettes/*.pdf
 
 # Settings files
 /*.DS_Store
+**/.DS_Store
 
 # pkdown
 docs

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: gDRtestData
 Title: gDRtestData - R data package with testing dose response data
-Version: 1.11.2
-Date: 2026-04-29
+Version: 1.11.3
+Date: 2026-06-01
 Description: R package with internal dose-response test data. Package provides functions to generate
   input testing data that can be used as the input for gDR pipeline. It also contains qs2 files
   with MAE data processed by gDR.

NEWS.md

@@ -1,3 +1,6 @@
+## gDRtestData 1.11.3 - 2026-06-01
+* add public data from DepMap Portal
+
 ## gDRtestData 1.11.2 - 2026-05-18
 * apply updated gDRstyle rules
 

R/dataset.R

@@ -0,0 +1,139 @@
+#' DepMap Models (Cell Line Metadata)
+#'
+#' Cell line information from DepMap Public 24Q4.
+#'
+#' @format Table
+#' \describe{
+#'   \item{ModelID}{Unique cell line identifier (ACH-XXXXX format)}
+#'   \item{CCLEName}{Cell line name from Cancer Cell Line Encyclopedia (CCLE)}
+#'   \item{CellLineName}{Common cell line name (e.g., "A375", "HCT-116")}
+#'   \item{TissueOrigin}{Indicates tissue model was derived from (Human, Mouse, Other)}
+#'   \item{DepmapModelType}{Abbreviated ID for model type. For cancer models, from Oncotree;
+#'   for other disease types, generated by DepMap}
+#'   \item{OncotreeLineage}{Primary cancer lineage classification (from Oncotree for cancer models,
+#'   generated by DepMap for others)}
+#'   \item{OncotreePrimaryDisease}{Primary disease of model (from Oncotree for cancer models,
+#'   generated by DepMap for others)}
+#'   \item{OncotreeSubtype}{Subtype classification of model (from Oncotree for cancer models,
+#'   generated by DepMap for others)}
+#'   \item{OncotreeCode}{Oncotree code for cancer models; left blank if
+#'   no corresponding code exists}
+#'   \item{PrimaryOrMetastasis}{Site of tumor origin (Primary/Metastatic/Recurrence/Other/Unknown)}
+#'   \item{Age}{Age at time of tissue sampling}
+#'   \item{AgeCategory}{Age category at time of sampling (Adult/Pediatric/Fetus/Unknown)}
+#'   \item{Sex}{Sex at time of sampling (Female/Male/Unknown)}
+#'   \item{PatientRace}{Patient/clinical indicated race (not derived)}
+#' }
+#'
+#' @source \url{https://depmap.org/portal/data_page/?tab=allData}
+#'
+#' @details
+#' Downloaded May 26, 2024 from DepMap Portal (version 24Q4).
+#'
+#' Citation: DepMap, Broad (2024). DepMap 24Q4 Public. Figshare+.
+#' https://doi.org/10.25452/figshare.plus.27993248.v1
+#'
+#' @docType data
+#' @keywords internal
+#' @name DepMap_Model
+NULL
+
+#' CRISPR Gene Effect Scores
+#'
+#' Genome-wide CRISPR/Cas9 knockout dependency scores.
+#'
+#' @format Matrix with cell lines as rows and genes as columns
+#'
+#' @source \url{https://depmap.org/portal/data_page/?tab=allData}
+#'
+#' @details
+#' - Rows: Cell line identifiers
+#' - Columns: NCBI gene IDs (Entrez format)
+#' - Values: Dependency scores (-1 to +1); lower = more essential
+#' - NA indicates insufficient screen coverage
+#'
+#' @docType data
+#' @keywords internal
+#' @name DepMap_CRISPRGeneEffect
+NULL
+
+
+#' Gene Expression (Log2 TPM)
+#'
+#' RNA-seq based gene expression for protein-coding genes.
+#'
+#' @format Matrix with ~1000 rows (cell lines) and ~19,000 columns (genes)
+#'
+#' @source \url{https://depmap.org/portal/data_page/?tab=allData}
+#'
+#' @details
+#' - Rows: Cell line identifiers
+#' - Columns: NCBI gene IDs (Entrez format)
+#' - Values: Log2(TPM + 1) transformed expression
+#' - Only protein-coding genes included
+#'
+#' @docType data
+#' @keywords internal
+#' @name DepMap_OmicsExpressionProteinCodingGenesTPMLogp1
+NULL
+
+
+#' Somatic Mutations (Hotspot)
+#'
+#' Binary matrix of known hotspot mutations from whole exome sequencing.
+#'
+#' @format Matrix with cell lines as rows and genes as columns
+#'
+#' @source \url{https://depmap.org/portal/data_page/?tab=allData}
+#'
+#' @details
+#' - Rows: Cell line identifiers
+#' - Columns: NCBI gene IDs
+#' - Values: Binary (0 = no mutation, 1 = hotspot mutation)
+#' - Hotspots defined by COSMIC and OncoKB
+#'
+#' @docType data
+#' @keywords internal
+#' @name DepMap_OmicsSomaticMutationsMatrixHotspot
+NULL
+
+
+#' Somatic Mutations (Damaging)
+#'
+#' Binary matrix of damaging mutations (frame-shift, stop-gain, splice-site).
+#'
+#' @format Matrix with cell lines as rows and genes as columns
+#'
+#' @source \url{https://depmap.org/portal/data_page/?tab=allData}
+#'
+#' @details
+#' - Rows: Cell line identifiers
+#' - Columns: NCBI gene IDs
+#' - Values: Binary (0 = no mutation, 1 = damaging mutation)
+#' - High-confidence loss-of-function mutations
+#'
+#' @docType data
+#' @keywords internal
+#' @name DepMap_OmicsSomaticMutationsMatrixDamaging
+NULL
+
+
+#' Copy Number Variation (CNV)
+#'
+#' Gene-level copy number estimates from SNP microarray or WES.
+#'
+#' @format Matrix with cell lines as rows and genes as columns
+#'
+#' @source \url{https://depmap.org/portal/data_page/?tab=allData}
+#'
+#' @details
+#' - Rows: Cell line identifiers
+#' - Columns: NCBI gene IDs
+#' - Values: Log2 ratio relative to diploid reference
+#' - Typical range: -2 (deletion) to +3 (amplification)
+#' - 0 = diploid (2 copies)
+#'
+#' @docType data
+#' @keywords internal
+#' @name DepMap_OmicsCNGene
+NULL

README.md

@@ -9,6 +9,8 @@ gDRtestData - R data package with testing dose response data to be used by all g
 
 - `inst/annotation_data/`	annotation data provided in the package
 
+- `inst/depmap_data/`	data from DepMap Portal (shorten)
+
 - `inst/scripts/`	scripts to generate example dataset
 
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