completeMatrix {oncoPredict}

This function performs an iterative matrix completion algorithm to predict drug response for pre-clinical data when there are missing ('NA') values.

Description

This function performs an iterative matrix completion algorithm to predict drug response for pre-clinical data when there are missing ('NA') values.

Usage

completeMatrix(senMat, nPerms = 50)

Arguments

senMat

A matrix of drug sensitivity data with missing ('NA') values. rownames() are samples (e.g. cell lines), and colnames() are drugs.

nPerms

The number of iterations that the EM-algorithm (expectation maximization approach) run. The default is 50, as previous findings recommend 50 iterations (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1050-9)

Value

A matrix of drug sensitivity scores without missing values. rownames() are samples, and colnames are drugs.