testGScogps: testGScogps

In OGSA: Outlier Gene Set Analysis

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)

OGSA documentation built on April 28, 2020, 6:58 p.m.