ZIP: Calculate Delta Synergy Score Based on ZIP Model

In shuyuzheng/synergyfinder: Calculate and Visualize Synergy Scores for Drug Combinations

Calculate Delta Synergy Score Based on ZIP Model

Description

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

Usage

ZIP(response, Emin = NA, Emax = NA, quiet = TRUE)

Arguments

response	A data frame. It must contain the columns: "conc1", "conc2", ..., for the concentration of the combined drugs and "response" for the observed %inhibition at certain combination.
Emin	The expected minimum response value in the 4 parameter log-logistic model.
Emax	The expected maximum response value in the 4 parameter log-logistic model.
quiet	A logical value. If it is TRUE then the warning message will not show during calculation.

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 data frame containing the concentrations for drugs, reference effect, fitted response and synergy score estimated by ZIP model.

Author(s)

• Shuyu Zheng [e-mail]

• Jing Tang [e-mail]

References

• Yadav B, Wennerberg K, Aittokallio T, Tang J. (2015). Searching for Drug Synergy in Complex Dose-Response Landscape Using an Interaction Potency Model. Comput Struct Biotechnol J, 13:504– 513.

Examples

# No single drug fitted modle before
data("mathews_screening_data")
data <- ReshapeData(mathews_screening_data)
response <- data$response[data$response$block_id == 1, 
                          c("conc1", "conc2", "response")]
ZIP_score <- ZIP(response)

## Not run: 
# Parallel processing:
if (future::supportsMulticore()) {
  future::plan(future::multicore)
} else {
  future::plan(future::multisession)
}
ZIP(response)
# future::plan(future::sequential) # Turn off the multicore setting

## End(Not run)

shuyuzheng/synergyfinder documentation built on Feb. 20, 2023, 11:33 p.m.