ZIP {synergyfinder} | R Documentation |
ZIP
calculates the Δ score matrix from a dose-response
matrix by using Zero Interaction Potency (ZIP) method.
ZIP(response.mat, quiet = TRUE, drug.row.model = NULL, drug.col.model = NULL)
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 |
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. |
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.
A matrix of Δ score calculated via Zero Interaction Potency (ZIP) method.
Liye He liye.he@helsinki.fi
Jing Tang jing.tang@helsinki.fi
Shuyu Zheng shuyu.zheng@helsinki.fi
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.
# 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.score2 <- ZIP(response.mat[-1, -1], drug.col.model=drug.col.model, drug.row.model=drug.row.model)