Prep table with metric values for single-agent experiment

Prep table with metric values for single-agent experiment

Usage

prep_dt_response_metric_sa(
  dt_metrics,
  d_name,
  normalization_type = "RV",
  metric = "xc50",
  fit_source = "gDR"
)

Arguments

dt_metrics

data.table representing data from the Metrics assay, outputted by gDRutils::convert_se_assay_to_dt and single-agent SummarizedExperiment

d_name

string with drug name to be plotted (identifiers DrugName)

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")

fit_source

string source name for metrics

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("sa")]]
dt_metrics <- gDRutils::convert_se_assay_to_dt(se = se,
                                               assay_name = "Metrics")
d_name <- "drug_004"
dt_response <- prep_dt_response_metric_sa(dt_metrics, d_name)
dt_response <-
  prep_dt_response_metric_sa(dt_metrics, d_name,
                             metric = c("xc50", "x_mean", "x_max"))

dt_averaged <- gDRutils::convert_se_assay_to_dt(se = se,
                                                assay_name = "Averaged")
dt_metrics_capped <-
  gDRutils::cap_assay_infinities(conc_assay_dt = dt_averaged,
                                 assay_dt = dt_metrics,
                                 experiment_name = gDRutils::get_supported_experiments("sa"),
                                 capping_fold = 5)
d_name <- "drug_026"
dt_response <- prep_dt_response_metric_sa(dt_metrics, d_name)
dt_response <-
  prep_dt_response_metric_sa(dt_metrics, d_name,
                             metric = c("xc50", "x_mean", "x_max"))