testGScogps {OGSA} | R Documentation |
Performs gene set test on outlier counts
testGScogps (outlierCts, geneSets)
outlierCts |
Vector with gene names and outlier counts |
geneSets |
List of gene sets |
A vector with rank sum gene set statistics
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
## 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)