Calculate the synergy scores for drug combinations

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Description

A function to calculate the synergy scores for drug combinations using different models.

Usage

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CalculateSynergy(data, method = "ZIP", correction = TRUE, Emin = 0,
  Emax = 100, nan.handle = c("LL4", "L4"))

Arguments

data

a list object generated by function ReshapeData

method

a parameter to specify which models to use to calculate the synergy scores. Choices are "ZIP", "Bliss", "HSA" and "Loewe". Defaults to "ZIP".

correction

a parameter to specify if 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. For "Bliss", "HSA" and "Loewe" model, it is used only when correction is required.

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. For "Bliss", "HSA" and "Loewe" model, it is used only when correction is required.

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 list of the following components:

dose.response.mats

the same as the input data component.

drug.pairs

the same as the input data component.

scores

a list of matrixes of synergy scores.

method

the method used to calculate the synergy scores.

Author(s)

Liye He liye.he@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)
scores <- CalculateSynergy(data)