getBinaryMutationData: Compute a binary gene mutation data matrix from SNP and other mutation event-level data.

Description

Compute a binary gene mutation data matrix from SNP and other mutation event-level data.

Usage

getBinaryMutationData(mutInfo, mutData, maxVariantFreq = 0.2,
  maxNormalPopulationFreq = 0.005, maxSiftScore = 0.05,
  minPolyPhenScore = 0.85)

Arguments

mutInfo

A data frame with the following named columns: Gene, the name of the gene associated with the mutation event; probe.ids, a unique identifier specifying the mutation event; SNP_1000_genome, the frequency of the mutation event in SNP 1000; ESP5400, the frequency of the mutation event in ESP5400; SNP_type, the type of mutation event, chosen from "MISSENSE", "FRAMESHIFT", "NONFRAMESHIFT", "NONSENSE", "SPLICING"; SIFT_score, the SIFT score; Polyphen_score, the POLYPHEN score. Rownames of mutInfo should be set to probe.ids, i.e., the unique mutation event specifier.

mutData

A matrix with event level mutation information, with SNPs, etc. along rows and samples along columns. Rownames of mutData should exactly match those of mutInfo. The i-th row of mutInfo should thus give detailed information for the mutation event with data specified in the i-th row of mutData.

maxVariantFreq

The maximum proportion of mutant samples (used to exclude frequently occuring events); default value = 0.2.

maxNormalPopulationFreq

The maximum freqency of a mutation in the normal population (used to exclude likely germline variants); default value = 0.005.

maxSiftScore

The maximum accepted SIFT score (used to exclude presumed non-deleterious mutations); default value = 0.05.

minPolyPhenScore

The minimum accepted POLYPHEN score (used to exclude presumed non-deleterious mutations); default value = 0.85.

Value

A binary gene mutation matrix, with genes along rows, samples along columns, and 1s indicating deleterious mutations.

concept

rcellminer