PharmacoGx (version 1.1.6)

drugSensitivitySig: Creates a signature representing the association between gene expression (or other molecular profile) and drug dose response, for use in drug sensitivity analysis.

Description

Given a Pharmacoset of the sensitivity experiment type, and a list of drugs, the function will compute a signature for the effect gene expression on the molecular profile of a cell. The function returns the estimated coefficient, 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

drugSensitivitySig(pSet, mDataType, drugs, features, sensitivity.measure = c("ic50_published", "auc_published", "ic50_recomputed", "auc_recomputed", "auc_recomputed_star"), molecular.summary.stat = c("mean", "median", "first", "last", "or", "and"), sensitivity.summary.stat = c("mean", "median", "first", "last"), returnValues = c("estimate", "pvalue", "fdr"), sensitivity.cutoff, nthread = 1, verbose = TRUE)

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.

features

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

sensitivity.measure

[character] which measure of the drug dose sensitivity should the function use for its computations? The current choices are 'ic50_published', 'auc_published', 'ic50_recomputed', 'auc_recomputed'.

molecular.summary.stat

What summary statistic should be used to summarize duplicates for cell line molecular profile measurements?

sensitivity.summary.stat

What summary statistic should be used to summarize duplicates for cell line sensitivity measurements?

returnValues

[character] Which of estimate, t-stat, p-value and fdr should the function return for each gene drug pair?

sensitivity.cutoff

Allows to provide upper and lower bounds to sensitivity measures in the cases where the values exceed physical values due to numerical or other errors.

nthread

[numeric] if multiple cores are available, how many cores should the computation be parallelized over?

verbose

[boolean] 'TRUE' if the warnings and other infomrative message shoud be displayed

Value

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

Examples

data(GDSCsmall)
drug.sensitivity <- drugSensitivitySig(GDSCsmall, mDataType="rna", 
             nthread=1, features = featureNames(GDSCsmall, "rna")[1])
print(drug.sensitivity)