idwas: This function will test every drug against CNA amplifications...

In oncoPredict: Drug Response Modeling and Biomarker Discovery

This function will test every drug against CNA amplifications or somatic mutations for your cancer type.

Description

This function will test every drug against CNA amplifications or somatic mutations for your cancer type.

Usage

idwas(drug_prediction, data, n = 10, cnv, folder = FALSE)

Arguments

drug_prediction	The drug prediction data. Must be a data frame. rownames are samples, colnames are drugs. Make sure sample names are of the same form as the sample names in your cnv or mutation data. e.g. if the rownames() are TCGA barcodes of the form TCGA-##-####-###, make sure your cnv/mutation data also uses samples in the form TCGA-##-####-###
data	The CNA amplification or mutation data. Must be a data frame. If you wish to use CNA data, use the output from map_cnv(), where rows are genes and columns are samples, or use data of similar form. If you wish to use mutation data, use the method for downloading mutation data outlined in the vignette, and make sure the TCGA barcodes use '-' instead of '.'; if you use another dataset (and don't download data from TCGA), make sure your data file includes the following columns: 'Variant_Classification', 'Hugo_Symbol', 'Tumor_Sample_Barcode'.
n	The minimum number of samples you want CNA amplifications or mutations to occur in. The default is 10 (arbitrarily chosen).
cnv	TRUE or FALSE. Indicate whether or not you would like to test CNA amplification data. If TRUE, you will test CNA amplifications. If FALSE, you will test mutation data.
folder	If TRUE, write IDWAS results to CSV files in the current working directory. The default is FALSE.

Value

Raw p-value and beta-values for CNA amplifications or somatic mutations.

Examples

drugPrediction <- data.frame(drug1=c(1, 2, 3),
                             drug2=c(2, 1, 3),
                             row.names=c("S1", "S2", "S3"))
mutationData <- data.frame(Variant_Classification=c("Missense_Mutation",
                                                    "Missense_Mutation",
                                                    "Missense_Mutation"),
                           Tumor_Sample_Barcode=c("S1", "S2", "S3"),
                           Hugo_Symbol=c("GENE1", "GENE1", "GENE2"))
idwas(drugPrediction, mutationData, n=1, cnv=FALSE)

oncoPredict documentation built on June 29, 2026, 5:07 p.m.