| Subset an AnnoBroadGseaRes object | [,AnnoBroadGseaRes,ANY,ANY,ANY-method |
| Subset a FisherResultList object by indexing | [,FisherResultList,ANY,missing,missing-method |
| Subset a FisherResultList object by namespace and name | [,FisherResultList,character,character,missing-method |
| Convert a list of AnnoBroadGseaResItem objects to a list | AnnoBroadGseaRes |
| Annotated BROAD GSEA Results for one contrast | AnnoBroadGseaRes-class |
| Convert a BroadGseaResItem object to an AnnoBroadGseaResItem object | AnnoBroadGseaResItem |
| Annotated BROAD GSEA result item | AnnoBroadGseaResItem-class |
| A list of AnnoBroadGseaRes objects | AnnoBroadGseaResList-class |
| Convert an FisherResultList object into a data.frame | as.data.frame,FisherResultList-method |
| An adapted and enhanced version of limma::camera | biosCamera |
| A S4 class representing the atom structure of results of the BROAD GSEA tool | BroadGseaResItem-class |
| Build the command-line command to run BROAD GSEA | buildBroadGSEAcomm |
| Run CAMERA method using EdgeResult | camera.EdgeResult |
| Run the CAMERA method using LimmaVoomResult | camera.LimmaVoomResult |
| Apply the CAMERA method to a DGEList object and a contrast | cameraDGEListByContrast |
| Apply the CAMERA method to a DGEList object | cameraLimmaVoomResultsByContrast |
| Convert a CAMERA table into a graph | cameraTable2graph |
| Perform gene-set enrichment (GSE) analysis | doGse |
| Expand genes in the CAMERA result table | expandCameraTableGenes |
| Make a factor vector from a character vector by the order of the parsed numbers | factorByNumberInStr |
| Return FDR values | fdrValue |
| Filter by size | filterBySize |
| Result of Fisher's exact test | FisherResult-class |
| A list of results of Fisher's exact test | FisherResultList-class |
| Fisher's method to combine multiple p-values | fishersMethod |
| Perform Fisher's exact test | fisherTest |
| Perform Fisher's exact test on a gene set | fisherTest,character,character,character-method |
| Perform Fisher's exact test on a GmtList object | fisherTest,character,GmtList,character-method |
| Perform Fisher's exact test on a GeneSet object | fisherTest,character,list,character-method |
| Run Fisher's exact test on an EdgeResult object | fisherTestEdgeResult |
| Append NewHitsProp to the result 'data.table' returned by 'fisherTest' | fisherTestResultNewHitsProp |
| GeMS base URL To set GeMS base URL in your environment, use `GeMS_BASE_URL=value` in your "~/.Renviron" file | GeMS_BASE_URL |
| GeMS genesets retrieval URL | GeMS_GENESETS_URL |
| GeMS insert URL | GeMS_INSERT_URL |
| GeMS remove URL | GeMS_REMOVE_URL |
| GeMS geneset retrieval URL for testing | GeMS_TEST_GENESETS_URL |
| GeMS URL for testing | GeMS_TEST_URL |
| Test gene set enrichment by permutating gene labels of statistics | geneSetPerm |
| A generic, virtual S4 class for gene-set analysis result | GeneSetResult-class |
| Get the name of the column which store false-discovery rates (adjusted P-values) from topTables | getFDRCol |
| Send a list as JSON query to an URL and fetch the response | getJsonResponse |
| Get the name of the column which store unadjusted P-values from topTables | getPvalCol |
| Get one or more gene-sets with their names | getSetsWithNamesFromGeMS |
| Get gene-sets for application | getSetsWithPropertyFromGeMS |
| Get one gene-set with its name | getSetWithNameFromGeMS |
| Get gene sets of a user from GeMS | getUserSetsFromGeMS |
| Return GSEA core enrichment genes (also known as leading-edge genes) | gseaCoreEnrichGenes gseaCoreEnrichGenes,AnnoBroadGseaRes-method gseaCoreEnrichGenes,AnnoBroadGseaResItem-method gseaLeadingEdgeGenes |
| Return GSEA core enrichment score threshold | gseaCoreEnrichThr gseaCoreEnrichThr,AnnoBroadGseaRes-method gseaCoreEnrichThr,BroadGseaResItem-method |
| Return GSEA enrichment scores | gseaES gseaES,AnnoBroadGseaRes-method gseaES,AnnoBroadGseaResList-method gseaES,BroadGseaResItem-method |
| Return GSEA enrichment score profile | gseaESprofile gseaESprofile,BroadGseaResItem-method |
| Return GSEA FDR | gseaFDR gseaFDR,AnnoBroadGseaRes-method gseaFDR,AnnoBroadGseaResList-method gseaFDR,BroadGseaResItem-method |
| Extract pathway fingerprints from GSEA results | gseaFingerprint gseaFingerprintMatrix |
| Return GSEA FWER values | gseaFWER gseaFWER,AnnoBroadGseaRes-method gseaFWER,AnnoBroadGseaResList-method gseaFWER,BroadGseaResItem-method |
| Return GSEA normalized enrichment scores | gseaNES gseaNES,AnnoBroadGseaRes-method gseaNES,AnnoBroadGseaResList-method gseaNES,BroadGseaResItem-method |
| Return GSEA number of permutation | gseaNP gseaNP,AnnoBroadGseaRes-method gseaNP,AnnoBroadGseaResList-method gseaNP,BroadGseaResItem-method |
| Read GSEA statistic for pathway fingerprinting | gseaResES gseaResQvalue |
| Extract scores from GSEA results | gseaScore gseaScores |
| Return the effective size of gene-set | gsEffectiveSize gsEffectiveSize,FisherResult-method gsEffectiveSize,FisherResultList-method |
| The core algorithm to perform Fisher's exact test on a gene set | gsFisherTestCore |
| Return gene-set gene count | gsGeneCount |
| Return gene-set gene indices | gsGeneIndices gsGeneIndices,BroadGseaResItem-method |
| Return gene-set genes | gsGenes gsGenes,AnnoBroadGseaRes-method gsGenes,AnnoBroadGseaResItem-method gsGenes,GmtList-method |
| gsGenes-set | gsGenes<- gsGenes<-,AnnoBroadGseaResItem,character-method |
| Return gene-set gene values | gsGeneValues gsGeneValues,AnnoBroadGseaRes-method gsGeneValues,AnnoBroadGseaResItem-method |
| gsGeneValues-set | gsGeneValues<- gsGeneValues<-,AnnoBroadGseaResItem,numeric-method |
| Core algorithm to perform Fisher's exact test on a list of gene set | gsListFisherTestCore |
| Return gene-set name | gsName gsName,AnnoBroadGseaRes-method gsName,BroadGseaResItem-method gsName,FisherResult-method gsName,FisherResultList-method gsName,GmtList-method |
| Return gene-set namespace | gsNamespace gsNamespace,FisherResult-method gsNamespace,FisherResultList-method gsNamespace,GmtList-method |
| Return the size (unique length) of gene-sets | gsSize |
| Return hits | hits hits,FisherResult-method hits,FisherResultList-method |
| Insert a GmtList object to GeMS | insertGmtListToGeMS |
| Construct message body to insert into GeMS | insertGmtListToGeMSBody |
| Test whether GeMS is reachable | isGeMSReachable |
| Return a vector of logical values, indicating whether genes belong to core enrichment or not | isGseaCoreEnrich |
| Return a logical vector indicating whether a gene-set is significantly enriched or not, given the FDR threshold | isSigGeneSet |
| S3 generic for kendallW | kendallW |
| Compute Kendall's W for an eSet object | kendallW.eSet |
| Compute Kendall's W for a matrix | kendallW.matrix |
| S3 generic for kendallW information | kendallWinfo kendallWinfo.matrix |
| S3 method to assign kendallW information to a matrix | kendallWinfo<-.matrix |
| Use Kendall's W and graph theory to assign independent measurements into sub-groups by correlation | kendallWmat |
| Cluster gene-sets by enrichment profiles with k-means clustering, and select representative gene-sets by gene-set composition | kmeansGeneset |
| Convert a one-level list into an adjacency matrix | list2mat |
| Perform the GAGE analysis for EdgeResult and GmtList | logFCgage |
| Merge CAMERA results using limma default parameters and biosCamera parameters | mergeCameraResults |
| Return the minimal FDR value from a FisherResultList | minFDRvalue |
| Return the minimal p-value from a FisherResultList | minPvalue |
| Wrap the gage::gage method to report consistent results as the CAMERA method | myGage |
| Order strings by numbers in them | orderByNumberInStr |
| Parse contributing genes by genesets from the result data.frame of the 'CAMERA' method | parseCameraContributingGenes |
| Parse contributing genes from the CAMERA output file | parseContributingGenes |
| Parse contributing genes by genesets | parseGenesetsContributingGenes |
| Parse an output directory of the Broad GSEA tool | parseGSEAdir |
| Pretty RONET Gene-set Names | prettyRonetGenesetNames |
| Print a FisherResult object | print.FisherResult |
| Print a FisherResultList object | print.FisherResultList |
| Print S3 object FishersMethodResult | print.FishersMethodResult |
| Print contributing genes | printContributingGenes |
| Return P-values | fdrValue,FisherResult-method fdrValue,FisherResultList-method pValue pValue,FisherResult-method pValue,FisherResultList-method |
| Read CAMERA results into a tibble object | readCameraResults |
| Read default genesets for gene-set enrichment analysis | readDefaultGenesets |
| Read molecular-phenotyping genesets | readMPSGmt |
| Read RONET GMT files with namespace information | readRonetGmt |
| Read significant CAMERA results into a tibble | readSigCameraResults |
| Read significant CAMERA results into a matrix | readSigCameraScoreMatrix |
| Rmove one or gene sets of the same source and user from GeMS | removeFromGeMS |
| Message body to remove one or gene sets of the same source and user from GeMS | removeFromGeMSBody |
| Extract gene-set namespace from RONET GMT files | ronetGeneSetNamespace |
| Show a anonBroadGseaRes object | show,AnnoBroadGseaRes-method |
| Show an AnnoBroadGseaResItem object | show,AnnoBroadGseaResItem-method |
| Show a BroadGseaResItem object | show,BroadGseaResItem-method |
| Return names of gene-sets that are significantly enriched given the FDR threshold | sigGeneSet |
| Return a data.frame of significantly enriched gene-sets | sigGeneSetTable |
| Return a data.frame of top gene-sets with the lowest p-values | topGeneSetTable |
| Return a data.frame of significantly enriched gene-sets with a minimum number | topOrSigGeneSetTable |
| Write an GmtList object into a file | writeGmt |
| Calculate mid-p quantile residuals | zscoreDGE |
