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| bggenes | Background sets of genes used in examples |
| bggenes_hum | Background sets of genes used in examples |
| convertToList | S4 class for GAFReader object |
| degenes | Differential expressed genes used in examples |
| degenes_hum | Differential expressed genes used in examples |
| down_annotobj | Precompiled objects of GeneGroups, FuncAnnotGroups classes used in examples |
| down_groups | Precompiled objects of GeneGroups, FuncAnnotGroups classes used in examples |
| examdata_bg | Background sets of genes used in examples |
| examdata_degs | Differential expressed genes used in examples |
| examdata_objs | Precompiled objects of GeneGroups, FuncAnnotGroups classes used in examples |
| fagroupstopgo_class | S4 class for FuncAnnotGroupsTopGO object |
| FoldSpecTest | FoldSpecTest S4 class |
| foldspectest_class | FoldSpecTest S4 class |
| FuncAnnotGroupsTopGO | S4 class for FuncAnnotGroupsTopGO object |
| GAFReader | S4 class for GAFReader object |
| gafreader_class | S4 class for GAFReader object |
| GeneGroups | S4 class for Gene Groups |
| genegroups_class | S4 class for Gene Groups |
| getAnnotation | Get annotation derived from annotation file |
| getAnnotation-method | Get annotation derived from annotation file |
| getFStable | FoldSpecTest S4 class |
| getFStable-method | FoldSpecTest S4 class |
| getGroups | S4 class for Gene Groups |
| getGroups-method | S4 class for Gene Groups |
| getIntNames | S4 class for Gene Groups |
| getIntNames-method | S4 class for Gene Groups |
| getNFStable | FoldSpecTest S4 class |
| getNFStable-method | FoldSpecTest S4 class |
| getQuanNumber | S4 class for Gene Groups |
| getQuanNumber-method | S4 class for Gene Groups |
| getRegType | S4 class for Gene Groups |
| getRegType-method | S4 class for Gene Groups |
| getResultList | S4 class for FuncAnnotGroupsTopGO object |
| getResultList-method | S4 class for FuncAnnotGroupsTopGO object |
| getResultTable | FoldSpecTest S4 class |
| getResultTable-method | FoldSpecTest S4 class |
| getVersion | S4 class for GAFReader object |
| getVersion-method | S4 class for GAFReader object |
| getWholeIntName | getWholeIntName S4 method |
| getWholeIntName-method | getWholeIntName S4 method |
| plot-method | Fold-change specific GO Profile chart plotting |
| rna_seq_data | Data from rna-seq experiment on auxin treatment of Arabidopsis thaliana roots |
| up_annotobj | Precompiled objects of GeneGroups, FuncAnnotGroups classes used in examples |
| up_groups | Precompiled objects of GeneGroups, FuncAnnotGroups classes used in examples |