ClusterPhenoTest {phenoTest} | R Documentation

## Test association of clusters with phenotype.

### Description

Test the associations between clusters that each sample belongs to (based on gene expression) and each phenotype.

### Usage

    ClusterPhenoTest(x,cluster,vars2test,B=10^4,p.adjust.method='none')

### Arguments

`x` | ExpressionSet with phenotype information stored in `pData(x)`.
`cluster` | variable of class `character` or `factor` telling at which cluster each sample belongs to.
`vars2test` | list with components 'continuous', 'categorical', 'ordinal' and 'survival' indicating which phenotype variables should be tested. 'continuous', 'categorical' and 'ordinal' must be character vectors, 'survival' a matrix with columns named 'time' and 'event'. The names must match names in `names(pData(x))`.
`B` | An integer specifying the number of replicates used in the chi-square Monte Carlo test (passed on to `chisq.test`).
`p.adjust.method` | Method for P-value adjustment, passed on to `p.adjust`.

### Details

Test association between the provided clusters and each phenotype.

For variables in vars2test\$continuous and vars2test\$ordinal a Kruskal-Wallis Rank Sum test is used; for vars2test\$categorical a chi-square test (with exact p-value if `simulate.p.value` is set to TRUE); for var2test\$survival a Cox proportional hazards likelihood-ratio test.

### Author(s)

David Rossell

### Examples

    #load data
    data(eset)
    eset

    #construct vars2test
    survival <- matrix(c("Relapse","Months2Relapse"),ncol=2,byrow=TRUE)
    colnames(survival) <- c('event','time')
    #add positive to have more than one category
    pData(eset)[1:20,'lymph.node.status'] <- 'positive'
    vars2test <- list(survival=survival,categorical='lymph.node.status')
    vars2test

    #first half of the samples will be one cluster and the rest the other cluster
    cluster <- c(rep('Cluster1',floor(ncol(eset)/2)),rep('Cluster2',ncol(eset)-floor(ncol(eset)/2)))

    #test association
    ClusterPhenoTest(eset,cluster,vars2test=vars2test)

[Package phenoTest version 1.28.0 Index]