ZIP: Delta synergy score based on zero interaction potency (ZIP)...

Description Usage Arguments Value Author(s) References Examples

Description

A function to calculate delta synergy score based on zero interaction potency (ZIP) model

Usage

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ZIP(response.mat, correction = TRUE, Emin = 0, Emax = 100,
  nan.handle = c("LL4", "L4"))

Arguments

response.mat

a dose-response matrix with concentrations as row names and column names

correction

a parameter to specify if the baseline correction is used or not. Defaults to TRUE.

Emin

the minimal effect of the drug used in the 4-parameter log-logistic function to fit the dose-response curve. If it is not NA, it is fixed the value assigned by the user. Defaults to 0.

Emax

the maximal effect of the drug used in the 4-parameter log-logistic function to fit the dose-response curve. If it is not NA, it is fixed the value assigned by the user. Defaults to 100.

nan.handle

a parameter to specify if L.4 function or LL.4 function is used when fitting with LL.4 produces NaNs.

Value

A matrix of delta scores for all the dose pairs for a drug combination. For a does pair with at least one zero concentration, 0 is used as the synergy score.

Author(s)

Liye He liye.he@helsinki.fi, Jing Tang jing.tang@helsinki.fi

References

Yadav B, Wennerberg K, Aittokallio T, Tang J. Searching for Drug Synergy in Complex Dose-Response Landscape Using an Interaction Potency Model. Computational and Structural Biotechnology Journal 2015; 13: 504-513.

Examples

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data("mathews_screening_data")
data <- ReshapeData(mathews_screening_data)
delta.score <- ZIP(data$dose.response.mats[[1]])

google/synergyfinderengineered documentation built on May 16, 2019, 2:31 a.m.