annotate: Function for Gene-Set Enrichment Analysis
In HTDA: HTDA (High Throughput Data Analysis)

1	annotate(object, annotation = "ath1121501", ont = "MF", pvalue = 0.5, entrez, entrezid)

`object`	Differentially expressed data generated from diffExp function
`annotation`	bioconductor annotation database default ath1121501
`ont`	ontology i.e MF,BP,CC default MF
`pvalue`	Significant cutoff default 0.05
`entrez`	yes or no
`entrezid`	if entrez is yes, then the entrez id object

The function calculate Gene-Set Enrichment Analysis (GSEA) using hyperg eometric t-test for both up and down regulated genes at a logfold cutoof 1 and - 1.

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (object, annotation = "ath1121501", ont = "MF", pvalue = 0.5, 
    entrez, entrezid) 
{
    up <- object@diffExp[which(object@diffExp$logFC >= 1), ]
    down <- object@diffExp[which(object@diffExp$logFC >= -1), 
        ]
    de <- rbind(up, down)
    geneUniverse <- rownames(object@qData)
    geneSample <- de$ID
    if (entrez == "no") {
        genesample1 <- entrezid[which(rownames(entrezid) %in% 
            geneSample), ]
        geneUniverse1 <- entrezid[which(rownames(entrezid) %in% 
            geneUniverse), ]
        params <- new("GOHyperGParams", geneIds = genesample1, 
            universeGeneIds = geneUniverse1, annotation = annotation, 
            ontology = ont, pvalueCutoff = pvalue, conditional = FALSE, 
            testDirection = "over")
        hgOver <- GOstats::hyperGTest(params)
    }
    else {
        params <- new("GOHyperGParams", geneIds = geneSample, 
            universeGeneIds = geneUniverse, annotation = annotation, 
            ontology = ont, pvalueCutoff = pvalue, conditional = FALSE, 
            testDirection = "over")
        hgOver <- GOstats::hyperGTest(params)
    }
    object@enrichment <- summary(hgOver)
    new("PreProcessData", object)
  }