ParCalculateTemplate: Parallel Calculate Drug Combination data in template format

In DrugComb/TidyComb: Preparing drug combination data for DrugComb

Parallel Calculate Drug Combination data in template format

Description

Parallel Calculate Drug Combination data in template format

Usage

ParCalculateTemplate(
  template,
  cores = 1,
  summary.only = FALSE,
  seed = NULL,
  ...
)

Arguments

template	a dataframe in the format as template. Columns "block_id", "drug_row", "drug_col", "inhibition", "conc_r", "conc_c", "conc_r_unit", "conc_c_unit","cell_line_name", "drug_row", "drug_col" are reqired.
cores	A integer. It indicates number of cores would be allocated to the parallel processed
summary.only	a logical value. If it is TRUE then only summary table is calculated and returned, otherwise, for tables will be return. Default setting is FALSE.
seed	a integer or NULL. It is used to set the random seed to AddNoise function to make sure the results are reproducible. By default, it is set as NULL which means no seed was set.
...	Other arguments required by nested functions. Some important arguments are: impute and noise inherited from function CalculateMat; method inherited from function CorrectBaseLine; Emin and Emax inherited from function FitDoseResponse.

Value

A list. It contains 4 tables:

• response It contains the modified inhibition value and 4 type of synergy scores of each drug dose response pair.

• summary It contains summarized information of each blocks: synergy scores, css, ri, S

• curve It contains the coefficients from single drug dose response curve.

• surface It contains the smoothed inhibition value and synergy scores of each drug dose response pair.

Author(s)

Jing Tang [e-mail] Shuyu Zheng [e-mail]

Examples

data <- read.csv(system.file("template.csv", package = "TidyComb"),
                 stringsAsFactors = FALSE)
res <- ParCalculateTemplate(data)

DrugComb/TidyComb documentation built on June 22, 2022, 2:49 a.m.