geneDrugPerturbation {ToxicoGx}

R Documentation

Compute gene-drug associations

Description

Function computing gene-drug associations from perturbation data

Usage

geneDrugPerturbation(x, concentration, type, batch, duration, model = FALSE)

Arguments

x	[numeric] Vector of gene expression values
concentration	[numeric] Vector with drug concentrations/doses
type	[factor] Vector of factors specifying the cell lines or type types
batch	[factor] Vector of factors specifying the batch
duration	[character] Vector of measurement times (in hours)
model	[logical] Should the full linear model be returned? Default set to FALSE

Value

[numeric] Vector reporting the effect size (estimateof the coefficient of drug concentration), standard error (se), sample size (n), t statistic, and F statistics and its corresponding p-value

Examples

ToxicoGx::drugPerturbationSig(tSet = TGGATESsmall,
  mDataType="rna",
  cell_lines="Hepatocyte",
  duration="24",
  dose=c("Control", "Low"),
  drugs=c("Omeprazole", "Isoniazid"),
  returnValues=c("estimate","tstat", "pvalue", "fdr"),
  verbose=FALSE)

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