Nothing
summary.gsaResult <- function(object,
mode = c("summary", "table"),
orderBy = c("adjustedPValues", "rawPValues", "geneSetName"),
significantOnly = FALSE,
signLevel = object$signLevel,
...){
if(!inherits(object,"gsaResult")){
stop("'object' mut be of class gsaResult.")
}
mode <- match.arg(mode)
if(mode == "summary"){
cat("\n Analysis: ", object$analysis$name, "\n", sep ="")
cat("\n ", length(object$rawPValues),
" gene set(s) tested:", "\n", sep ="")
cat(" - ", sum(object$rawPValues < object$signLevel),
" gene set(s) with raw p-value < ",
object$signLevel, "\n", sep ="")
cat(" - min p-value: ",
names(object$res.all)[which.min(object$rawPValues)], " (", min(object$rawPValues), ")", "\n\n", sep ="")
cat(" ", "Correction for multiple testing: ",
object$adjustmentMethod, "\n", sep ="")
cat(" - ", sum(object$adjustedPValues < object$signLevel),
" gene set(s) with adjusted p-value < ",
object$signLevel, "\n\n", sep ="")
}else{
print(createSummaryTable(object,
orderBy = orderBy,
significantOnly = significantOnly,
signLevel = signLevel))
}
return(invisible(NULL))
}
createSummaryTable <- function(object,
orderBy = c("adjustedPValues", "rawPValues", "geneSetName"),
significantOnly = FALSE,
signLevel = object$signLevel){
if(!inherits(object,"gsaResult")){
stop("'object' mut be of class gsaResult.")
}
orderBy <- match.arg(orderBy)
#determine intersect size
intersects <- sapply(object$res.all, function(i){
return(length(i$geneSetValues$intersectGeneSetCoreSet))
})
#if all intersect sizes are 0 no fisher test has been performed and
#the sizes must not be printed
if(sum(intersects) == 0){
res <- data.frame(geneSetName = names(object$res.all),
adjustedPValues = object$adjustedPValues,
rawPValues = object$rawPValues,
geneSetSize = sapply(object$res.all, function(i){return(length(i$geneSet))}),
stringsAsFactors=FALSE)
}else{
res <- data.frame(geneSetName = names(object$res.all),
adjustedPValues = object$adjustedPValues,
rawPValues = object$rawPValues,
geneSetSize = sapply(object$res.all, function(i){return(length(i$geneSet))}),
intersectSize = intersects,
stringsAsFactors=FALSE)
}
#order table according to parameter
indOrdered <- order(res[[orderBy]])
res <- res[indOrdered,]
if(significantOnly){
ind <- which(res[["adjustedPValues"]] < signLevel)
res <- res[ind,]
}
rownames(res) <- NULL
return(res)
}
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