CalculateSynergy: Calculate the Synergy Scores for Drug Combinations

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

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) from one dose-response matrix.

Usage

CalculateSynergy(
  data,
  method = c("ZIP", "HSA", "Bliss", "Loewe"),
  Emin = NA,
  Emax = NA,
  adjusted = TRUE,
  correct_baseline = "non",
  iteration = 10,
  seed = 123
)

Arguments

data	A list object generated by function ReshapeData.
method	A vector of characters. It is used to specify the reference models used to calculate the synergy scores. Choices are "ZIP", "Bliss", "HSA" and "Loewe". Default setting is to calculate all the available models.
Emin	The expected minimum response value in the 4 parameter log-logistic model. It is used while calling ZIP and Loewe.
Emax	The expected maximum response value in the 4 parameter log-logistic model. It is used while calling ZIP and Loewe.
adjusted	A logical value. If it is TRUE, the 'response' column in the table 'data$response' will be used to calculate synergy scores. If it is FALSE, the raw data 'response_origin' column 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 value. 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 1 or 2 elements into inputted data list:

• scores A data frame. It contains synergy scores, reference effects and fitted response values (only for "ZIP" model) calculated by selected method. If there are replicates in the block, the mean values across all iterations for all the metrics mentioned above will be output.

• scores_statistics A data frame. It will be output if there is block have replicated response values. It contains the the statistics (including mean, standard deviation, standard error of mean and 95 and fitted response values (only for "ZIP" model) across results from iterations.

This function also add mean of synergy scores across whole combination matrix to the data$drug_pair table.

Author(s)

• Shuyu Zheng [e-mail]

• Jing Tang [e-mail]

Examples

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

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