# Package for Fold-specific GO Terms Recognition

## Documentation for package ‘FoldGO’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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