`RS` <-
function(sigvals, geneids,
database="GO", functionalCategories=NULL, species="Hs",
min.g=10, minGenesInCategory=NULL,
max.g=NA, maxGenesInCategory=NULL,
sig.cutoff=0.1, sigFDR=NULL,
averageMultipleProbes=TRUE,
allGenesInCategoriesAsBackground=FALSE,
two.sided=FALSE, na.rm=TRUE,
verbose=TRUE) {
## sanity checks etc.
if(!missing(database)) {
warning("Argument `database` deprecated. Please use `functionalCategories` instead.")
if(missing(functionalCategories)) functionalCategories <- database
}
if (is.null(functionalCategories)) functionalCategories <- "GO"
if(!(missing(min.g) & missing(max.g))) {
warning("Argument `min.g`, `max.g` deprecated. Please use `minGenesInCategory`, `maxGenesInCategory` instead.")
if(missing(minGenesInCategory)) minGenesInCategory <- min.g
if(missing(maxGenesInCategory)) maxGenesInCategory <- max.g
}
if(!missing(sig.cutoff)) {
warning("Argument `sig.cutoff` deprecated. Please use `sigFDR` instead.")
if(missing(sigFDR)) sigFDR <- sig.cutoff
}
RandomSet(sigvals=sigvals,
geneids=geneids,
functionalCategories=functionalCategories,
species=species,
minGenesInCategory=minGenesInCategory,
maxGenesInCategory=maxGenesInCategory,
sigFDR=sigFDR,
averageMultipleProbes=averageMultipleProbes,
allGenesInCategoriesAsBackground=allGenesInCategoriesAsBackground,
two.sided=two.sided,
na.rm=na.rm,
verbose=verbose)
}
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