Load DepMap merged data for one selected feature

Usage

prep_dt_depmap_feat(
  feat_data_path,
  meta_data_path,
  feature_set = "CRISPRGeneEffect",
  with_decoding = FALSE
)

Arguments

feat_data_path: string with path to the directory containing the molecular feature set file to load from DepMap.
meta_data_path: string with path to metadata file describing all cancer models/cell lines which are referenced by a dataset contained within the DepMap portal. It is usually a file named Model.csv or Model.csv.gz.
feature_set: string containing the name of the molecular feature set to load from DepMap. This name should also correspond to the file containing the feature data (without the extension, which is assumed to be csv or csv.gz)
with_decoding: logical whether the feature OmicsArmLevelCNA, OmicsSomaticMutationsMatrixHotspot and OmicsSomaticMutationsMatrixDamaging should be encoded into a 0-1 scheme

Value

A named list with elements, that may be input to prep_dt_assoc

dt_depmap data.table with feature data from DepMap (wide format),.
selected_feat_meta_col string name of feature.

Examples

feat_data_path <- system.file("depmap_data", package = "gDRtestData")
meta_data_path <- system.file("depmap_data/Model.csv.gz", package = "gDRtestData")
dt_depmap_feat <- prep_dt_depmap_feat(feat_data_path = feat_data_path,
                                      meta_data_path = meta_data_path)