getBinaryMutationData {rcellminer} | R Documentation

## 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.

[Package rcellminer version 2.12.1 Index]