Prep table with metric values for combination experiment

Usage

prep_dt_response_metric_diff(
  dt_metrics,
  d_name,
  d_name2,
  cellline1 = NULL,
  cellline2 = NULL,
  normalization_type = "RV",
  metric = "xc50",
  fit_source = "gDR",
  additional_cols = NULL
)

Arguments

dt_metrics: data.table representing data from the Metrics assay, outputted by gDRutils::convert_se_assay_to_dt and combo SummarizedExperiment
d_name: string representing the drug name to be plotted (identifier DrugName). If set to NULL, the function will return a table for all available DrugName
d_name2: string representing the drug name to be plotted (identifier DrugName_2). If set to NULL, the function will return a table for all available DrugName_2
cellline1: string representing the first cell line name. If set to NULL, the function will return a table for all available cell lines.
cellline2: string representing the second cell line name. If set to NULL, the function will return a table for all available cell lines.
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"), "x_mean" ("GR Mean" or "RV Mean") "ec50" ("GEC50" or "EC50") or "x_AOC_range" ("GR AOC within set range" or "RV AOC within set range")
fit_source: string source name for metrics
additional_cols: character vector with additional cols that should be included in the output

Value

data.table with selected metric, input to prep_dt_assoc

Examples

mae <- gDRutils::get_synthetic_data("combo_matrix_small")
se <- mae[[gDRutils::get_supported_experiments("combo")]]
dt_metrics <- gDRutils::convert_se_assay_to_dt(se = se,
                                               assay_name = "Metrics")
d_name <- "drug_004"
d_name2 <- "drug_026"
dt_response <-
  prep_dt_response_metric_diff(dt_metrics, d_name, d_name2,
  metric = c("xc50", "x_mean", "x_max"))

cellline1 <- "cellline_GB"
cellline2 <- "cellline_HB"

dt_response <-
  prep_dt_response_metric_diff(dt_metrics, d_name = NULL, d_name2 = NULL,
  cellline1, cellline2,
  metric = c("xc50", "x_mean", "x_max"))