Prep matrix with metric value based on the Metrics assay

Usage

prep_pheatmap_matrix(
  dt_response,
  normalization_type = "GR",
  metric = "xc50",
  fit_source = "gDR",
  experiment_type = gDRutils::get_supported_experiments("sa")
)

Arguments

dt_response: data.table representing data from the Metrics assay, outputted by gDRutils::convert_se_assay_to_dt and single-agent SummarizedExperiment or data.table representing data from the scores assay, outputted by gDRutils::convert_se_assay_to_dt and combo SummarizedExperiment
normalization_type: string with normalization types to be selected one of: "GR" ("GRvalue") or "RV" ("RelativeViability")
metric: string name of the metric; one of: "xc50" ("GR50" or "IC50" - respectively depending on normalization_type), "x_max" ("GR Max" or "E Max") or "x_mean" ("GR Mean" or "RV Mean"); but the values from any numeric column can be displayed.
fit_source: string source name for metrics
experiment_type: string with experiment name; one of: "single-agent", "combination" or "co-dilution"

Value

matrix with values for selected metric with CellLinName in the rows and DrugName (or combination of DrugName and DrugName_2) in the columns

Author

Janina Smoła janina.smola@external.roche.com

Examples

mae <- gDRutils::get_synthetic_data("combo_matrix")
se <- mae[[gDRutils::get_supported_experiments("sa")]]
dt_metrics <- gDRutils::convert_se_assay_to_dt(se = se,
                                               assay_name = "Metrics")

mat <- prep_pheatmap_matrix(dt_response = dt_metrics,
                            experiment_type = gDRutils::get_supported_experiments("sa"))

mae <- gDRutils::get_synthetic_data("combo_matrix")
se <- mae[[gDRutils::get_supported_experiments("combo")]]
dt_scores <- gDRutils::convert_se_assay_to_dt(se = se,
                                              assay_name = "scores")

mat <- prep_pheatmap_matrix(dt_response = dt_scores,
                            metric = "hsa_score",
                            normalization_type = "RV",
                            experiment_type = gDRutils::get_supported_experiments("combo"))