testGScogps {OGSA} | R Documentation

## testGScogps

### Description

Performs gene set test on outlier counts

### Usage

    testGScogps (outlierCts, geneSets)

### Arguments

`outlierCts` | Vector with gene names and outlier counts
`geneSets` | List of gene sets

### Value

A vector with rank sum gene set statistics

### References

Ochs, M. F., Farrar, J. E., Considine, M., Wei, Y., Meshinchi, S., & Arceci, R. J. (n.d.). Outlier Analysis and Top Scoring Pair for Integrated Data Analysis and Biomarker Discovery. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 1-1. doi:10.1109/tcbb.2013.153

### Examples

    ## Not run:
    data(ExampleData)
    data('_BC_GS')

    #Set up your phenotype
    phenotype <- rep(0, 69)
    phenotype[annot[, 3] == 'Event'] <- 1
    names(phenotype) <- rownames(annot)

    # set up values for expr-meth-cnv in that order
    tailLRL <- c('left', 'right', 'left')

    dataSet <- list(expr, meth, cnv)

    tibLRLcorr <- copaInt(dataSet, phenotype, tails=tailLRL, corr=TRUE)
    gsTibLRLcorr <- testGScogps(tibLRLcorr, pathGS)

    ## End(Not run)

[Package OGSA version 1.12.0 Index]