Nothing
## this is for OBO
## the function orderedAttr() is defined
## in GOHyperGResults-accessors.R
setMethod("pvalues", signature(r="OBOHyperGResult"),
function(r) orderedAttr(r, "pvalue"))
setMethod("oddsRatios", signature(r="OBOHyperGResult"),
function(r) orderedAttr(r, "oddsRatio"))
setMethod("expectedCounts", signature(r="OBOHyperGResult"),
function(r) orderedAttr(r, "expCount"))
## the function entrezGeneIdUniverse() is defined
## in GOHyperGResults-accessors.R
setMethod("geneIdUniverse", signature(r="OBOHyperGResult"),
function(r, cond=TRUE) {
if (cond && conditional(r))
nodeData(r@goDag, n=nodes(r@goDag)[r@pvalue.order],
attr="condGeneIds")
else
entrezGeneUniverse(r)
})
setMethod("summary", signature(object="OBOHyperGResult"),
function(object, pvalue=pvalueCutoff(object),
categorySize=NULL) {
df <- callNextMethod(object=object, pvalue=pvalue,
categorySize=categorySize)
if (nrow(df) == 0) {
df$Term <- character(0)
return(df)
}
oboIds <- df[[1]]
df$Term <- object@gscDescriptions[oboIds]
df
})
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