CalculateTemplate: Calculate Drug Combination data in template format

In DrugComb/TidyComb: Preparing drug combination data for DrugComb

Calculate Drug Combination data in template format

Description

Calculate Drug Combination data in template format

Usage

CalculateTemplate(template, summary.only = FALSE, seed = NULL)

Arguments

template	a dataframe which must contains following columns: block_id: (integer) the identifier for a drug combination. If mul-tiple drug combinations are present, e.g. in the standard 384-well platewhere 6 drug combinations are fitted, then the identifiers for each of themmust be unique. drug_col: (character) the name of the drug on the columns in adose-response matrix. drug_row: (character) the name of the drug on the rows in adose-response matrix. conc_c: (numeric) the concentrations of the column drugs in a combination. conc_r: (numeric) the concentrations of the row drugs in a combination. conc_c_unit: (character) the unit of concentrations of the column drugs. It is typically nM or μM. conc_r_unit: (character) the unit of concentrations of the row drugs. It is typically nM or μM. response: (numeric) the effect of drug combinations at the concentra-tions specified by conc_r and conc_c. The effect must be normalized to %inhibition based on the positive and negative controls. For a well-controlled experiment, the range of the response values is expected from 0 to 100. However, missing values or extreme values are allowed. cell_line_name: (character) the name of cell lines on which the drug combination was tested.
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.

Value

A list. It contains 4 tables:

• response It contains the modified response 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 response 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 <- CalculateTemplate(data)

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