drugPerturbationSig: Creates a signature representing gene expression (or other...

In bhklab/PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

Creates a signature representing gene expression (or other molecular profile) change induced by administrating a drug, for use in drug effect analysis.

Description

Given a Pharmacoset of the perturbation experiment type, and a list of drugs, the function will compute a signature for the effect of drug concentration on the molecular profile of a cell. The algorithm uses a regression model which corrects for experimental batch effects, cell specific differences, and duration of experiment to isolate the effect of the concentration of the drug applied. The function returns the estimated coefficient for concentration, the t-stat, the p-value and the false discovery rate associated with that coefficient, in a 3 dimensional array, with genes in the first direction, drugs in the second, and the selected return values in the third.

Usage

drugPerturbationSig(
  pSet,
  mDataType,
  drugs,
  cells,
  features,
  nthread = 1,
  returnValues = c("estimate", "tstat", "pvalue", "fdr"),
  verbose = FALSE
)

Arguments

pSet	PharmacoSet a PharmacoSet of the perturbation experiment type
mDataType	character which one of the molecular data types to use in the analysis, out of dna, rna, rnaseq, snp, cnv
drugs	character a vector of drug names for which to compute the signatures. Should match the names used in the PharmacoSet.
cells	character a vector of cell names to use in computing the signatures. Should match the names used in the PharmacoSet.
features	character a vector of features for which to compute the signatures. Should match the names used in correspondant molecular data in PharmacoSet.
nthread	numeric if multiple cores are available, how many cores should the computation be parallelized over?
returnValues	character Which of estimate, t-stat, p-value and fdr should the function return for each gene drug pair?
verbose	logical(1) Should diagnostive messages be printed? (default false)

Value

list a 3D array with genes in the first dimension, drugs in the second, and return values in the third.

Examples

data(CMAPsmall)
drug.perturbation <- drugPerturbationSig(CMAPsmall, mDataType="rna", nthread=1)
print(drug.perturbation)

bhklab/PharmacoGx documentation built on April 18, 2024, 3:13 a.m.