geneDrugPerturbation: Compute gene-drug associations

In bhklab/ToxicoGx: Analysis of Large-Scale Toxico-Genomic Data

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)

bhklab/ToxicoGx documentation built on March 18, 2023, 6:44 a.m.