apply_combo_isobolograms

Compute Loewe combination index isobolograms for a combination SE, writing results to the isobolograms and all_iso_points assays. This is step 4 of the fit_SE.combinations pipeline.

Usage

apply_combo_isobolograms(
  se,
  series_identifiers = NULL,
  normalization_types = c("GR", "RV"),
  averaged_assay = "Averaged",
  metrics_assay = "Metrics",
  isobolograms_assay = "isobolograms",
  iso_points_assay = "all_iso_points"
)

Arguments

se

SummarizedExperiment with Averaged and Metrics assays.

series_identifiers

character vector of length 2. Defaults to get_default_nested_identifiers(se, ...).

normalization_types

character vector. Default c("GR", "RV").

averaged_assay

string. Default "Averaged".

metrics_assay

string. Default "Metrics".

isobolograms_assay

string; name of the Loewe curves output assay. Default "isobolograms".

iso_points_assay

string; name of the iso points output assay. Default "all_iso_points".

Value

Updated SE with isobolograms_assay and iso_points_assay assays.

Details

Requires the Averaged and Metrics assays (as produced by apply_combo_sa_fits or fit_SE.combinations). Isobologram analysis is only performed when at least 9 combo concentration points are available — otherwise NA is written, matching fit_SE.combinations behaviour.

See also

apply_combo_sa_fits, apply_combo_excess, apply_combo_scores, fit_SE.combinations

Examples

mae <- gDRutils::get_synthetic_data("finalMAE_combo_matrix_small")
combo_se <- mae[[gDRutils::get_supported_experiments("combo")]]
combo_se_iso <- apply_combo_isobolograms(combo_se[1, 1])
"isobolograms" %in% SummarizedExperiment::assayNames(combo_se_iso)
#> [1] TRUE