Man pages for bedapub/ribiosGSEA
Gene-Set Enrichment Analysis Tools in Ribios
| AnnoBroadGseaRes | Convert a list of AnnoBroadGseaResItem objects to a list |
| AnnoBroadGseaRes-class | Annotated BROAD GSEA Results for one contrast |
| AnnoBroadGseaResItem | Convert a BroadGseaResItem object to an AnnoBroadGseaResItem... |
| AnnoBroadGseaResItem-class | Annotated BROAD GSEA result item |
| AnnoBroadGseaResList-class | A list of AnnoBroadGseaRes objects |
| as.data.frame-FisherResultList-method | Convert an FisherResultList object into a data.frame |
| biosCamera | An adapted and enhanced version of limma::camera |
| BroadGseaResItem-class | A S4 class representing the atom structure of results of the... |
| buildBroadGSEAcomm | Build the command-line command to run BROAD GSEA |
| cameraDGEListByContrast | Apply the CAMERA method to a DGEList object and a contrast |
| camera.EdgeResult | Run CAMERA method using EdgeResult |
| camera.LimmaVoomResult | Run the CAMERA method using LimmaVoomResult |
| cameraLimmaVoomResultsByContrast | Apply the CAMERA method to a DGEList object |
| cameraTable2graph | Convert a CAMERA table into a graph |
| doGse | Perform gene-set enrichment (GSE) analysis |
| expandCameraTableGenes | Expand genes in the CAMERA result table |
| factorByNumberInStr | Make a factor vector from a character vector by the order of... |
| fdrValue | Return FDR values |
| filterBySize | Filter by size |
| FisherResult-class | Result of Fisher's exact test |
| FisherResultList-class | A list of results of Fisher's exact test |
| fishersMethod | Fisher's method to combine multiple p-values |
| fisherTest | Perform Fisher's exact test |
| fisherTest-character-character-character-method | Perform Fisher's exact test on a gene set |
| fisherTest-character-GmtList-character-method | Perform Fisher's exact test on a GmtList object |
| fisherTest-character-list-character-method | Perform Fisher's exact test on a GeneSet object |
| fisherTestEdgeResult | Run Fisher's exact test on an EdgeResult object |
| fisherTestResultNewHitsProp | Append NewHitsProp to the result 'data.table' returned by... |
| GeMS_BASE_URL | GeMS base URL To set GeMS base URL in your environment, use... |
| GeMS_GENESETS_URL | GeMS genesets retrieval URL |
| GeMS_INSERT_URL | GeMS insert URL |
| GeMS_REMOVE_URL | GeMS remove URL |
| GeMS_TEST_GENESETS_URL | GeMS geneset retrieval URL for testing |
| GeMS_TEST_URL | GeMS URL for testing |
| geneSetPerm | Test gene set enrichment by permutating gene labels of... |
| GeneSetResult-class | A generic, virtual S4 class for gene-set analysis result |
| getFDRCol | Get the name of the column which store false-discovery rates... |
| getJsonResponse | Send a list as JSON query to an URL and fetch the response |
| getPvalCol | Get the name of the column which store unadjusted P-values... |
| getSetsWithNamesFromGeMS | Get one or more gene-sets with their names |
| getSetsWithPropertyFromGeMS | Get gene-sets for application |
| getSetWithNameFromGeMS | Get one gene-set with its name |
| getUserSetsFromGeMS | Get gene sets of a user from GeMS |
| gseaCoreEnrichGenes | Return GSEA core enrichment genes (also known as leading-edge... |
| gseaCoreEnrichThr | Return GSEA core enrichment score threshold |
| gseaES | Return GSEA enrichment scores |
| gseaESprofile | Return GSEA enrichment score profile |
| gseaFDR | Return GSEA FDR |
| gseaFingerprint | Extract pathway fingerprints from GSEA results |
| gseaFWER | Return GSEA FWER values |
| gseaNES | Return GSEA normalized enrichment scores |
| gseaNP | Return GSEA number of permutation |
| gseaResES | Read GSEA statistic for pathway fingerprinting |
| gseaScore | Extract scores from GSEA results |
| gsEffectiveSize | Return the effective size of gene-set |
| gsFisherTestCore | The core algorithm to perform Fisher's exact test on a gene... |
| gsGeneCount | Return gene-set gene count |
| gsGeneIndices | Return gene-set gene indices |
| gsGenes | Return gene-set genes |
| gsGenes-set | gsGenes-set |
| gsGeneValues | Return gene-set gene values |
| gsGeneValues-set | gsGeneValues-set |
| gsListFisherTestCore | Core algorithm to perform Fisher's exact test on a list of... |
| gsName | Return gene-set name |
| gsNamespace | Return gene-set namespace |
| gsSize | Return the size (unique length) of gene-sets |
| hits | Return hits |
| insertGmtListToGeMS | Insert a GmtList object to GeMS |
| insertGmtListToGeMSBody | Construct message body to insert into GeMS |
| isGeMSReachable | Test whether GeMS is reachable |
| isGseaCoreEnrich | Return a vector of logical values, indicating whether genes... |
| isSigGeneSet | Return a logical vector indicating whether a gene-set is... |
| kendallW | S3 method for kendallW |
| kendallW.eSet | Compute Kendall's W for an eSet object |
| kendallWinfo | S3 method for kendallW information |
| kendallWmat | Use Kendall's W and graph theory to assign independent... |
| kendallW.matrix | Compute Kendall's W for a matrix |
| kmeansGeneset | Cluster gene-sets by enrichment profiles with k-means... |
| list2mat | Convert a one-level list into an adjacency matrix |
| logFCgage | Perform the GAGE analysis for EdgeResult and GmtList |
| mergeCameraResults | Merge CAMERA results using limma default parameters and... |
| minFDRvalue | Return the minimal FDR value from a FisherResultList |
| minPvalue | Return the minimal p-value from a FisherResultList |
| myGage | Wrap the gage::gage method to report consistent results as... |
| orderByNumberInStr | Order strings by numbers in them |
| parseCameraContributingGenes | Parse contributing genes by genesets from the result... |
| parseContributingGenes | Parse contributing genes from the CAMERA output file |
| parseGenesetsContributingGenes | Parse contributing genes by genesets |
| parseGSEAdir | Parse an output directory of the Broad GSEA tool |
| prettyRonetGenesetNames | Pretty RONET Gene-set Names |
| printContributingGenes | Print contributing genes |
| print.FisherResult | Print a FisherResult object |
| print.FisherResultList | Print a FisherResultList object |
| print.FishersMethodResult | Print S3 object FishersMethodResult |
| pValue | Return P-values |
| readCameraResults | Read CAMERA results into a tibble object |
| readDefaultGenesets | Read default genesets for gene-set enrichment analysis |
| readMPSGmt | Read molecular-phenotyping genesets |
| readRonetGmt | Read RONET GMT files with namespace information |
| readSigCameraResults | Read significant CAMERA results into a tibble |
| readSigCameraScoreMatrix | Read significant CAMERA results into a matrix |
| reexports | Objects exported from other packages |
| removeFromGeMS | Rmove one or gene sets of the same source and user from GeMS |
| removeFromGeMSBody | Message body to remove one or gene sets of the same source... |
| ribiosGSEA-package | The ribiosGSEA package |
| ronetGeneSetNamespace | Extract gene-set namespace from RONET GMT files |
| show-AnnoBroadGseaResItem-method | Show an AnnoBroadGseaResItem object |
| show-AnnoBroadGseaRes-method | Show a anonBroadGseaRes object |
| show-BroadGseaResItem-method | Show a BroadGseaResItem object |
| sigGeneSet | Return names of gene-sets that are significantly enriched... |
| sigGeneSetTable | Return a data.frame of significantly enriched gene-sets |
| sub-AnnoBroadGseaRes-ANY-ANY-ANY-method | Subset an AnnoBroadGseaRes object |
| sub-FisherResultList-ANY-missing-missing-method | Subset a FisherResultList object by indexing |
| sub-FisherResultList-character-character-missing-method | Subset a FisherResultList object by namespace and name |
| topGeneSetTable | Return a data.frame of top gene-sets with the lowest p-values |
| topOrSigGeneSetTable | Return a data.frame of significantly enriched gene-sets with... |
| writeGmt | Write an GmtList object into a file |
| zscoreDGE | Calculate mid-p quantile residuals |
