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 1.10.0 Index]