computeUnivariateTernaryMatrix {divergence} | R Documentation

## Compute the ternary matrix with digitized divergence coding

### Description

Function for obtaining the ternary form for a matrix of data given a baseline range

### Usage

    computeUnivariateTernaryMatrix(seMat, Baseline)

### Arguments

`seMat` | SummariziedExperiment with an assay in [0, 1], with each column corresponding to a sample and each row corresponding to a feature; usually in quantile form.
`Baseline` | A list with a data frame element "Ranges" containing the baseline range of each features; this corresponds to the output of findUnivariateGammaWithSupport() or computeUnivariateSupport()

### Value

A matrix containing the ternary form data.

### Examples

    baseMat = breastTCGA_Mat[, breastTCGA_Group == "NORMAL"]
    seMat.base = SummarizedExperiment(assays=list(data=baseMat))
    assays(seMat.base)$quantile = computeQuantileMatrix(seMat.base)
    baseline = computeUnivariateSupport(seMat=seMat.base)
    dataMat = breastTCGA_Mat[, breastTCGA_Group != "NORMAL"]
    seMat = SummarizedExperiment(assays=list(data=dataMat))
    assays(seMat)$quantile = computeQuantileMatrix(seMat)
    assays(seMat)$div = computeUnivariateTernaryMatrix(seMat=seMat, Baseline=baseline)

[Package divergence version 1.0.0 Index]