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the BROAD GSEA tool", "topics": [ "BroadGseaResItem-class" ] }, { "page": "buildBroadGSEAcomm", "title": "Build the command-line command to run BROAD GSEA", "topics": [ "buildBroadGSEAcomm" ] }, { "page": "camera.EdgeResult", "title": "Run CAMERA method using EdgeResult", "topics": [ "camera.EdgeResult" ] }, { "page": "camera.LimmaVoomResult", "title": "Run the CAMERA method using LimmaVoomResult", "topics": [ "camera.LimmaVoomResult" ] }, { "page": "cameraDGEListByContrast", "title": "Apply the CAMERA method to a DGEList object and a contrast", "topics": [ "cameraDGEListByContrast" ] }, { "page": "cameraLimmaVoomResultsByContrast", "title": "Apply the CAMERA method to a DGEList object", "topics": [ "cameraLimmaVoomResultsByContrast" ] }, { "page": "cameraTable2graph", "title": "Convert a CAMERA table into a graph", "topics": [ "cameraTable2graph" ] }, { "page": "doGse", "title": "Perform gene-set enrichment (GSE) analysis", "topics": [ "doGse" ] }, { "page": "expandCameraTableGenes", "title": "Expand genes in the CAMERA result table", "topics": [ "expandCameraTableGenes" ] }, { "page": "factorByNumberInStr", "title": "Make a factor vector from a character vector by the order of the parsed numbers", "topics": [ "factorByNumberInStr" ] }, { "page": "fdrValue", "title": "Return FDR values", "topics": [ "fdrValue" ] }, { "page": "filterBySize", "title": "Filter by size", "topics": [ "filterBySize" ] }, { "page": "FisherResult-class", "title": "Result of Fisher's exact test", "topics": [ "FisherResult-class" ] }, { "page": "FisherResultList-class", "title": "A list of results of Fisher's exact test", "topics": [ "FisherResultList-class" ] }, { "page": "fishersMethod", "title": "Fisher's method to combine multiple p-values", "topics": [ "fishersMethod" ] }, { "page": "fisherTest", "title": "Perform Fisher's exact test", "topics": [ "fisherTest" ] }, { "page": "fisherTest-character-character-character-method", "title": "Perform Fisher's exact test on a gene set", "topics": [ "fisherTest,character,character,character-method" ] }, { "page": "fisherTest-character-GmtList-character-method", "title": "Perform Fisher's exact test on a GmtList object", "topics": [ "fisherTest,character,GmtList,character-method" ] }, { "page": "fisherTest-character-list-character-method", "title": "Perform Fisher's exact test on a GeneSet object", "topics": [ "fisherTest,character,list,character-method" ] }, { "page": "fisherTestEdgeResult", "title": "Run Fisher's exact test on an EdgeResult object", "topics": [ "fisherTestEdgeResult" ] }, { "page": "fisherTestResultNewHitsProp", "title": "Append NewHitsProp to the result 'data.table' returned by 'fisherTest'", "topics": [ "fisherTestResultNewHitsProp" ] }, { "page": "GeMS_BASE_URL", "title": "GeMS base URL To set GeMS base URL in your environment, use `GeMS_BASE_URL=value` in your \"~/.Renviron\" file", "topics": [ "GeMS_BASE_URL" ] }, { "page": "GeMS_GENESETS_URL", "title": "GeMS genesets retrieval URL", "topics": [ "GeMS_GENESETS_URL" ] }, { "page": "GeMS_INSERT_URL", "title": "GeMS insert URL", "topics": [ "GeMS_INSERT_URL" ] }, { "page": "GeMS_REMOVE_URL", "title": "GeMS remove URL", "topics": [ "GeMS_REMOVE_URL" ] }, { "page": "GeMS_TEST_GENESETS_URL", "title": "GeMS geneset retrieval URL for testing", "topics": [ "GeMS_TEST_GENESETS_URL" ] }, { "page": "GeMS_TEST_URL", "title": "GeMS URL for testing", "topics": [ "GeMS_TEST_URL" ] }, { "page": "geneSetPerm", "title": "Test gene set enrichment by permutating gene labels of statistics", "topics": [ "geneSetPerm" ] }, { "page": "GeneSetResult-class", "title": "A generic, virtual S4 class for gene-set analysis result", "topics": [ "GeneSetResult-class" ] }, { "page": "getFDRCol", "title": "Get the name of the column which store false-discovery rates (adjusted P-values) from topTables", "topics": [ "getFDRCol" ] }, { "page": "getJsonResponse", "title": "Send a list as JSON query to an URL and fetch the response", "topics": [ "getJsonResponse" ] }, { "page": "getPvalCol", "title": "Get the name of the column which store unadjusted P-values from topTables", "topics": [ "getPvalCol" ] }, { "page": "getSetsWithNamesFromGeMS", "title": "Get one or more gene-sets with their names", "topics": [ "getSetsWithNamesFromGeMS" ] }, { "page": "getSetsWithPropertyFromGeMS", "title": "Get gene-sets for application", "topics": [ "getSetsWithPropertyFromGeMS" ] }, { "page": "getSetWithNameFromGeMS", "title": "Get one gene-set with its name", "topics": [ "getSetWithNameFromGeMS" ] }, { "page": "getUserSetsFromGeMS", "title": "Get gene sets of a user from GeMS", "topics": [ "getUserSetsFromGeMS" ] }, { "page": "gseaCoreEnrichGenes", "title": "Return GSEA core enrichment genes (also known as leading-edge genes)", "topics": [ "gseaCoreEnrichGenes", "gseaCoreEnrichGenes,AnnoBroadGseaRes-method", "gseaCoreEnrichGenes,AnnoBroadGseaResItem-method", "gseaLeadingEdgeGenes" ] }, { "page": "gseaCoreEnrichThr", "title": "Return GSEA core enrichment score threshold", "topics": [ "gseaCoreEnrichThr", "gseaCoreEnrichThr,AnnoBroadGseaRes-method", "gseaCoreEnrichThr,BroadGseaResItem-method" ] }, { "page": "gseaES", "title": "Return GSEA enrichment scores", "topics": [ "gseaES", "gseaES,AnnoBroadGseaRes-method", "gseaES,AnnoBroadGseaResList-method", "gseaES,BroadGseaResItem-method" ] }, { "page": "gseaESprofile", "title": "Return GSEA enrichment score profile", "topics": [ "gseaESprofile", "gseaESprofile,BroadGseaResItem-method" ] }, { "page": "gseaFDR", "title": "Return GSEA FDR", "topics": [ "gseaFDR", "gseaFDR,AnnoBroadGseaRes-method", "gseaFDR,AnnoBroadGseaResList-method", "gseaFDR,BroadGseaResItem-method" ] }, { "page": "gseaFingerprint", "title": "Extract pathway fingerprints from GSEA results", "topics": [ "gseaFingerprint", "gseaFingerprintMatrix" ] }, { "page": "gseaFWER", "title": "Return GSEA FWER values", "topics": [ "gseaFWER", "gseaFWER,AnnoBroadGseaRes-method", "gseaFWER,AnnoBroadGseaResList-method", "gseaFWER,BroadGseaResItem-method" ] }, { "page": "gseaNES", "title": "Return GSEA normalized enrichment scores", "topics": [ "gseaNES", "gseaNES,AnnoBroadGseaRes-method", "gseaNES,AnnoBroadGseaResList-method", "gseaNES,BroadGseaResItem-method" ] }, { "page": "gseaNP", "title": "Return GSEA number of permutation", "topics": [ "gseaNP", "gseaNP,AnnoBroadGseaRes-method", "gseaNP,AnnoBroadGseaResList-method", "gseaNP,BroadGseaResItem-method" ] }, { "page": "gseaResES", "title": "Read GSEA statistic for pathway fingerprinting", "topics": [ "gseaResES", "gseaResQvalue" ] }, { "page": "gseaScore", "title": "Extract scores from GSEA results", "topics": [ "gseaScore", "gseaScores" ] }, { "page": "gsEffectiveSize", "title": "Return the effective size of gene-set", "topics": [ "gsEffectiveSize", "gsEffectiveSize,FisherResult-method", "gsEffectiveSize,FisherResultList-method" ] }, { "page": "gsFisherTestCore", "title": "The core algorithm to perform Fisher's exact test on a gene set", "topics": [ "gsFisherTestCore" ] }, { "page": "gsGeneCount", "title": "Return gene-set gene count", "topics": [ "gsGeneCount" ] }, { "page": "gsGeneIndices", "title": "Return gene-set gene indices", "topics": [ "gsGeneIndices", "gsGeneIndices,BroadGseaResItem-method" ] }, { "page": "gsGenes", "title": "Return gene-set genes", "topics": [ "gsGenes", "gsGenes,AnnoBroadGseaRes-method", "gsGenes,AnnoBroadGseaResItem-method", "gsGenes,GmtList-method" ] }, { "page": "gsGenes-set", "title": "gsGenes-set", "topics": [ "gsGenes<-", "gsGenes<-,AnnoBroadGseaResItem,character-method" ] }, { "page": "gsGeneValues", "title": "Return gene-set gene values", "topics": [ "gsGeneValues", "gsGeneValues,AnnoBroadGseaRes-method", "gsGeneValues,AnnoBroadGseaResItem-method" ] }, { "page": "gsGeneValues-set", "title": "gsGeneValues-set", "topics": [ "gsGeneValues<-", "gsGeneValues<-,AnnoBroadGseaResItem,numeric-method" ] }, { "page": "gsListFisherTestCore", "title": "Core algorithm to perform Fisher's exact test on a list of gene set", "topics": [ "gsListFisherTestCore" ] }, { "page": "gsName", "title": "Return gene-set name", "topics": [ "gsName", "gsName,AnnoBroadGseaRes-method", "gsName,BroadGseaResItem-method", "gsName,FisherResult-method", "gsName,FisherResultList-method", "gsName,GmtList-method" ] }, { "page": "gsNamespace", "title": "Return gene-set namespace", "topics": [ "gsNamespace", "gsNamespace,FisherResult-method", "gsNamespace,FisherResultList-method", "gsNamespace,GmtList-method" ] }, { "page": "gsSize", "title": "Return the size (unique length) of gene-sets", "topics": [ "gsSize" ] }, { "page": "hits", "title": "Return hits", "topics": [ "hits", "hits,FisherResult-method", "hits,FisherResultList-method" ] }, { "page": "insertGmtListToGeMS", "title": "Insert a GmtList object to GeMS", "topics": [ "insertGmtListToGeMS" ] }, { "page": "insertGmtListToGeMSBody", "title": "Construct message body to insert into GeMS", "topics": [ "insertGmtListToGeMSBody" ] }, { "page": "isGeMSReachable", "title": "Test whether GeMS is reachable", "topics": [ "isGeMSReachable" ] }, { "page": "isGseaCoreEnrich", "title": "Return a vector of logical values, indicating whether genes belong to core enrichment or not", "topics": [ "isGseaCoreEnrich" ] }, { "page": "isSigGeneSet", "title": "Return a logical vector indicating whether a gene-set is significantly enriched or not, given the FDR threshold", "topics": [ "isSigGeneSet" ] }, { "page": "kendallW", "title": "S3 generic for kendallW", "topics": [ "kendallW" ] }, { "page": "kendallW.eSet", "title": "Compute Kendall's W for an eSet object", "topics": [ "kendallW.eSet" ] }, { "page": "kendallW.matrix", "title": "Compute Kendall's W for a matrix", "topics": [ "kendallW.matrix" ] }, { "page": "kendallWinfo", "title": "S3 generic for kendallW information", "topics": [ "kendallWinfo", "kendallWinfo.matrix" ] }, { "page": "kendallWinfo-set-.matrix", "title": "S3 method to assign kendallW information to a matrix", "topics": [ 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