CalculateSynergy {synergyfinder}R Documentation

Calculate the synergy scores for drug combinations

Description

CalculateSynergy is the main function for calculating synergy scores based on model(ZIP, Bliss, Loewe, and HSA) fron one dose-response matrix.

Usage

CalculateSynergy(data, method = "ZIP", adjusted = TRUE,
  data.type = "viability")

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".

adjusted

a logical value. If it is TRUE, the 'adjusted.response.mats' will be used to calculate synergy scores. If it is FALSE, the raw data ('dose.response.mats') will be used to calculate synergy scores.

data.type

a parameter to specify the response data type which can be either "viability" or "inhibition".

Details

The steps for calculation:

  1. Pre-process Matrix

    1. Impute for missing values (with the average of values from the nearest four cells) in original matrix by using function ImputeNA.

    2. Add noise(A small random number ranging from 0 to 0.001) to original matrix by using function line{AddNoise}. )

    3. Correct baseline to 0, if correction is TRUE.

  2. Calculate synergy scores using the functions:

Value

a list. It contains 4 elements:

Author(s)

Examples

data("mathews_screening_data")
data <- ReshapeData(mathews_screening_data)
scores <- CalculateSynergy(data)

[Package synergyfinder version 1.10.2 Index]