ZIP {synergyfinder}R Documentation

Calculate Delta synergy score based on ZIP model

Description

ZIP calculates the Δ score matrix from a dose-response matrix by using Zero Interaction Potency (ZIP) method.

Usage

ZIP(response.mat, quiet = TRUE, drug.row.model = NULL,
  drug.col.model = NULL)

Arguments

response.mat

A drug cobination dose-response matrix. It's column name and row name are representing the concerntrations of drug added to column and row, respectively. The values in matrix indicate the inhibition rate to cell growth.

quiet

A logical value. If it is TRUE then the warning message will not show during calculation.

drug.row.model

(optional) a character. It indicates the model type used for fitting dose-response curve for drug added to rows.

drug.col.model

(optional) a character. It indicates the model used for fitting dose-response curve for drug added to columns.

Details

Zero Interaction Potency (ZIP) is a reference model for evaluating the conbimation effect of two drugs. It captures the effect of drug combination by comparing the change in the potency of the dose-response curves between individual drugs and their combinations.

The optional arguments drug.col.model, drug.row.model are designed for reuse the single drug dose response model fitting results, if it has been down before. Functions FitDoseResponse and ExtractSingleDrug could be used to calculate these arguments.

Value

A matrix of Δ score calculated via Zero Interaction Potency (ZIP) method.

Author(s)

References

Examples

# No single drug fitted modle before
data("mathews_screening_data")
data <- ReshapeData(mathews_screening_data)
response.mat <- data$dose.response.mats[[1]]
ZIP.score <- ZIP(response.mat)

# Single drug dose response models have been fitted before.
drug.row.model <- FitDoseResponse(ExtractSingleDrug(response.mat, dim="row"))
drug.col.model <- FitDoseResponse(ExtractSingleDrug(response.mat, dim="col"))

ZIP.score <- ZIP(response.mat, drug.col.model=drug.col.model,
                 drug.row.model=drug.row.model)

[Package synergyfinder version 1.10.5 Index]