Drug Response Modeling and Biomarker Discovery

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Documentation for package ‘oncoPredict’ version 1.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

calcPhenotype	Generate predicted drug sensitivity scores
completeMatrix	This function performs an iterative matrix completion algorithm to predict drug response for pre-clinical data when there are missing ('NA') values.
doVariableSelection	Remove genes with low variation.
glds	This function determines drug-gene associations for pre-clinical data.
homogenizeData	Homogenizes two expression matrices
idwas	This function will test every drug against every CNV or somatic mutation for your cancer type.
map_cnv	This function maps cnv data to genes. The output of this function is a .RData file called map.RData; this file contains theCnvQuantVecList_mat (rows are genes, and columns are samples) and tumorSamps (indicates which samples are primary tumor samples, 01A).
summarizeGenesByMean	Average over duplicate gene values