CalculateSensitivity: Calculate the Sensitivity Scores for Drug Combinations

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

Calculate the Sensitivity Scores for Drug Combinations

Description

CalculateSensitivity is the main function for calculating sensitivity scores from the dose response matrix. It will return the RI (relative inhibition), IC50 (relative IC50) for each drug in the combination. It will also calculate the CSS (combination sensitivity score) for each drug while other drugs are at their IC50 and the CSS for the whole combination matrix.

Usage

CalculateSensitivity(
  data,
  adjusted = TRUE,
  correct_baseline = "non",
  iteration = 10,
  seed = 123
)

Arguments

data	A list object generated by function ReshapeData.
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.
correct_baseline	A character value. It indicates the method used for baseline correction. Available values are: non No baseline correction. part Adjust only the negative values in the matrix. all Adjust all values in the matrix.
iteration	An integer. It indicates the number of iterations for bootstrap on data with replicates.
seed	An integer or NULL. It is used to set the random seed in synergy scores calculation on data with replicates.

Value

This function will add columns into data$drug_pairs table. The columns are:

• ic50_1/2/... Relative IC50 for drug 1, 2, ...

• ri_1/2/... Relative Inhibition (RI) for drug 1, 2, ...

• css1_ic502/... CSS score of drug 1 while fixing drug 2 at its IC50.

• css Over all CSS score for the whole block. It's the mean value of the CSS for all drug pairs in the combination.

If there are replicates in the block, this function will add one table named as "sensitivity_scores_statistics" for the statistics of the values mentioned about into the input data list.

Author(s)

• Shuyu Zheng [e-mail]

• Jing Tang [e-mail]

Examples

data("ONEIL_screening_data")
data <- ReshapeData(ONEIL_screening_data, data_type = "inhibition")
data <- CalculateSensitivity(data)

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