getDrugGeneData: Function to generate heatmaps that show a drugs influence on...

Description Usage Arguments Value Examples

View source: R/getDrugGeneData.R

Description

This function returns a heat map that shows how a drug changes the expression of a set of genes, as determined by molecular profiles in the pharmacoSet supplied.

Usage

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getDrugGeneData(drugPert, pharmSet, mDataType, drugName, genesOfInt)

Arguments

drugPert

the drug perturbation signature of interest

pharmSet

the pharmacoSet used to generate the drug perturbation signature

mDataType

the type of molecular data to obtain from the PharmacoSet (see PharmacoGx::molecularProfiles)

drugName

the name of the drug one would like to inspect for its effect on the supplied genes

genesOfInt

a character vector containing the names of the genes one would like to observe the drugs effect on

Value

a list containing 1. beforeDrugMat which is a matrix containing the expression levels for the genes before the drug was applied. 2. afterDrugMat which is a matrix containing the expression levels for the genes before the drug was applied. 3. geneChangePlot, which is a levelplot object showing the change in expression for the genes due to the drugs

Examples

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data("drugPertEx")
#example in getSigGeneVolPlot function yields below genes
drivingGenes = c("ABCC5", "VPS28", "RPS6KA2", "TRIM2", "CD47", "MELK", "CDKN3", "GGH", "MCM7", "KIF2C")

bhklab/CMapBox documentation built on Nov. 6, 2019, 8:07 p.m.