drugSensitivitySig {PharmacoGx}R Documentation

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, cells, tissues,
  sensitivity.measure = "auc_recomputed",
  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, standardize = c("SD", "rescale", "none"),
  molecular.cutoff = NA, molecular.cutoff.direction = c("less",
  "greater"), 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.

cells

[character] allows choosing exactly which cell lines to include for the signature fitting. Should be a subset of cellNames(pSet)

tissues

[character] a vector of which tissue types to include in the signature fitting. Should be a subset of cellInfo(pSet)$tissueid

sensitivity.measure

[character] which measure of the drug dose sensitivity should the function use for its computations? Use the sensitivityMeasures function to find out what measures are available for each PSet.

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

[numeric] Allows the user to binarize the sensitivity data using this threshold.

standardize

[character] One of "SD", "rescale", or "none", for the form of standardization of the data to use. If "SD", the the data is scaled so that SD = 1. If rescale, then the data is scaled so that the 95 interquantile range lies in [0,1]. If none no rescaling is done.

molecular.cutoff

Allows the user to binarize the sensitivity data using this threshold.

molecular.cutoff.direction

[character] One of "less" or "greater", allows to set direction of binarization.

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

...

additional arguments not currently fully supported by the function

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 = fNames(GDSCsmall, "rna")[1])
print(drug.sensitivity)


[Package PharmacoGx version 1.14.0 Index]