getDrugsImpactOnGenes: Function to generate heatmaps that show a drugs influence on...
In bhklab/CMapBox:

Description Usage Arguments Value Examples

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.

1 2	getDrugsImpactOnGenes(drugPert, pharmSet, mDataType, drugName, genesOfInt, makePlot = TRUE)

`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
`makePlot`	a boolean specifying whether to generate the plot showing the gene expression changes due to the drug. Default is TRUE

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

data("drugPertEx")
data("psetSub")
#example in getSigGeneVolPlot function yields below genes
drivingGenes = c("ABCC5", "VPS28", "RPS6KA2", "TRIM2", "CD47", "MELK", "CDKN3", "GGH", "MCM7", "KIF2C")
plotAndMats = getDrugsImpactOnGenes(drugPert = drugPertEx, pharmSet = psetSub, mDataType = "rna", drugName = "BRD-K78431006", genesOfInt = drivingGenes)