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

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)
#> PharmacoSet Name:  CMAP 
#> Signature Type:  Perturbation 
#> Date Created:  Tue Apr 16 19:03:57 2024 
#> Number of Drugs:  5 
#> Number of Genes/Probes:  51