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

In PharmacoGx: Analysis of Large-Scale Pharmacogenomic Data

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	[bool] 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)

PharmacoGx documentation built on Feb. 28, 2021, 2 a.m.