## ----available Schemas, message=FALSE, warning=FALSE-------------------------- library("AnnotationForge") available.dbschemas() ## ----Acquire annotation data, message=FALSE----------------------------------- library("org.Hs.eg.db") frame = toTable(org.Hs.egGO) goframeData = data.frame(frame$go_id, frame$Evidence, frame$gene_id) head(goframeData) ## ----transformGOFrame, message=FALSE, warning=FALSE--------------------------- goFrame=GOFrame(goframeData,organism="Homo sapiens") goAllFrame=GOAllFrame(goFrame) ## ----Make GSC, message=FALSE-------------------------------------------------- library("GSEABase") gsc <- GeneSetCollection(goAllFrame, setType = GOCollection()) ## ----make parameter, message=FALSE-------------------------------------------- library("GOstats") universe = Lkeys(org.Hs.egGO) genes = universe[1:500] params <- GSEAGOHyperGParams(name="My Custom GSEA based annot Params", geneSetCollection=gsc, geneIds = genes, universeGeneIds = universe, ontology = "MF", pvalueCutoff = 0.05, conditional = FALSE, testDirection = "over") ## ----call HyperGTest---------------------------------------------------------- Over <- hyperGTest(params) head(summary(Over)) ## ----KEGGFrame object--------------------------------------------------------- frame = toTable(org.Hs.egPATH) keggframeData = data.frame(frame$path_id, frame$gene_id) head(keggframeData) keggFrame=KEGGFrame(keggframeData,organism="Homo sapiens") ## ----KEGG Parameters---------------------------------------------------------- gsc <- GeneSetCollection(keggFrame, setType = KEGGCollection()) universe = Lkeys(org.Hs.egGO) genes = universe[1:500] kparams <- GSEAKEGGHyperGParams(name="My Custom GSEA based annot Params", geneSetCollection=gsc, geneIds = genes, universeGeneIds = universe, pvalueCutoff = 0.05, testDirection = "over") kOver <- hyperGTest(params) head(summary(kOver)) ## ----info--------------------------------------------------------------------- sessionInfo()