Man pages for guokai8/richR
Function Enrichment analysis and Network construction
| Annot-class | Class "Annot" This class represents the Annotation... |
| batchGSEAplot | Create multiple GSEA plots for different comparisons |
| buildAnnot-methods | make annotation database |
| buildMSIGDB | Download database from Msigdb and prepare for enrichment... |
| buildOwn | make annotation database using bioAnno results |
| comparedot | draw dotplot for multiple enrichment results |
| compareGSEA | compare GSEA enrichment results across different samples and... |
| compareResult | compare enrichment results across different samples |
| detail | detail generic |
| dollar-methods | S4 '$' accessors for Annot and richResult |
| dot-calculate_Enrichment_Score | calculate enrichment score |
| dot-clean.char | Remove newlines |
| dot-getmsig | msigdb support species |
| dot-ggcluster_enrich | Plot KEGG Cluster Visualization |
| dot-ggcluster_gsea | Plot KEGG Cluster Visualization |
| dot-kappa | kappa function |
| dot-kappa_cluster_internal | calculate kappa cluster |
| dot-makeGOdata | make GO annotation data function |
| dot-makeKOdata | make KEGG annotation data function |
| dot-makeKOMdata | make KEGG module annotation data function |
| dot-makeROdata | make Reactome annotation data function |
| dot-merge_term | merge term |
| dot-paste.char | Insert newlines after every n words (defaults to 4) |
| enrich | enrich method |
| enrich-ANY-Annot-method | Enrichment analysis function |
| enrich-ANY-data.frame-method | Enrichment analysis function |
| enrich_internal | Enrichment analysis for any type of annotation data |
| filterPathways | Filter pathways by multiple criteria |
| getann | build annotaion for kegg |
| getdetail | get detail and integrate with the input gene information |
| getPathways | Get available pathways from GSEA results |
| getPathwayStats | Get pathway statistics summary |
| ggbar | barplot for Enrichment results |
| ggbar-methods | ggbar method |
| ggcluster | Plot KEGG Cluster Visualization |
| ggdot | dotplot for Enrichment results |
| ggdot_internal | Dotplot for enrichment results |
| ggdot-methods | ggdot method |
| ggGSEA | plot the gsea result |
| ggheatmap | Plot compare heatmap of Enrichment result among DEG groups |
| ggnetmap | generate network based on Enrichment results |
| ggnetplot | richplot for Enrichment result |
| ggnetplot-method | ggnetplot method |
| ggnetplot-richResult-method | richplot for Enrichment results |
| ggnetwork | generate network based on Enrichment results |
| ggnetwork-methods | ggnetwork method |
| ggrich_internal | richplot |
| GO_child | Get all children terms of node |
| GSEAResult-class | Class "GSEAResult" This class represents the result from GSEA... |
| idconvert | Convert ID between ENTREZID to SYMBOL or other type ID based... |
| msigdbinfo | Print MSIGDB infomation |
| overlap | ovelap |
| parGSEA | GSEA Enrichment analysis function for data frame with log2FC... |
| plotGSEA | plot multiple significant pathways with enhanced... |
| rbind.GSEAResult | rbind generic function for GSEAResult object |
| rbind.richResult | rbind generic function for richResult object |
| reexports | Objects exported from other packages |
| result | result generic |
| result_detail_methods | S4 methods for result() and detail() on richResult and... |
| reverseList_bk | reverse List |
| richCluster | kappa cluster analysis |
| richCluster-data.frame-method | kappa cluster analysis |
| richCluster-richResult-method | kappa cluster analysis |
| richDAVID | Functional enrichment analysis with DAVID |
| richGO | GO Enrichment analysis function |
| richGO-ANY-Annot-method | GO Enrichment analysis function |
| richGO-ANY-data.frame-method | GO Enrichment analysis function |
| richGO_internal | GO Enrichment analysis function |
| richGSEA-ANY-Annot-method | GSEA Enrichment analysis function |
| richGSEA-ANY-data.frame-method | GSEA Enrichment analysis function |
| richGSEA_internal | Enrichment analysis for any type of annotation data |
| richGSEA-methods | richGSEA method |
| richKEGG | KEGG Enrichment analysis function |
| richKEGG-ANY-Annot-method | KEGG Enrichment analysis function |
| richKEGG-ANY-data.frame-method | KEGG Pathway Enrichment analysis function |
| richKEGG_internal | KEGG Pathway Enrichment analysis function |
| richLevel-ANY-Annot-method | Pathway Enrichment analysis for different level function |
| richLevel-ANY-data.frame-method | Pathway Enrichment analysis for different level function |
| richLevel_internal | Pathway Enrichment analysis for different level function |
| richLevel-methods | richLevel method |
| richResult-class | Class "richResult" This class represents the result of... |
| s4-accessors | S4 row- and column-related methods for Annot, richResult,... |
| saveGSEAplot | Save GSEA plot with optimal dimensions |
| searchPathways | Search pathways by keyword |
| showData | show avaliable data based on bioconductor annotation package |
| subset-methods | S4 subsetting methods for Annot, richResult, and GSEAResult |
| summary-GSEAResult-method | S4 summary method for GSEAResult objects |
| summary-richResult-method | S4 summary method for richResult objects |
| utilities-methods | S4 methods for head, tail, dim on Annot, richResult,... |
| vec_to_df | vector to data.frame |
