ToxicoGx (version 0.1.1)

drugPerturbationSig: Drug perturbation analysis

Description

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

Usage

drugPerturbationSig(
  tSet,
  mDataType,
  drugs = NULL,
  cell_lines = NULL,
  features = NULL,
  duration = NULL,
  dose = NULL,
  nthread = 1,
  returnValues = c("estimate", "tstat", "pvalue", "fdr"),
  verbose = FALSE
)

Arguments

tSet

ToxicoSet a ToxicoSet 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 (only rna currently supported)

drugs

character a vector of drug names for which to compute the signatures. Should match the names used in the ToxicoSet.

cell_lines

character a vector of cell names to use in computing the signatures. Should match the names used in the ToxicoSet.

features

character a vector of features for which to compute the signatures. Should match the names used in correspondant molecular data in ToxicoSet.

duration

character a vector of experiment durations for which to inlcude in the computed the signatures.

dose

character a vector of dose levels to include in the results

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

ToxicoSig An object composed of a 3D array with genes in the first dimension, drugs in the second, and return values in the third.

Details

Given a Toxicoset of the perturbation experiment type, and a character vector 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.

Examples

# NOT RUN {
if (interactive()) {
data(TGGATESsmall)
drug.perturbation <- drugPerturbationSig(TGGATESsmall, mDataType="rna",
 features = head(fNames(TGGATESsmall, "rna")), nthread=1)
}

# }