# Gene Set Enrichment Analysis Extended to Contingency Cubes

## Documentation for package ‘geecc’ version 1.20.0

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

## Help Pages

geecc-package | Gene set enrichment for two or three categories
concub-class | Class '"concub"'
concubfilter-class | Class '"concubfilter"'
drop.insignif.layer | Class '"concubfilter"'
drop.insignif.layer-method | Class '"concubfilter"'
drop.insignif.layer<- | Class '"concubfilter"'
drop.insignif.layer<--method | Class '"concubfilter"'
drop.lowl2or.layer | Class '"concubfilter"'
drop.lowl2or.layer-method | Class '"concubfilter"'
drop.lowl2or.layer<- | Class '"concubfilter"'
drop.lowl2or.layer<--method | Class '"concubfilter"'
drop.wrongdir.layer | Class '"concubfilter"'
drop.wrongdir.layer-method | Class '"concubfilter"'
drop.wrongdir.layer<- | Class '"concubfilter"'
drop.wrongdir.layer<--method | Class '"concubfilter"'
filterConCub | Filter results from two- or three-way tests
geecc | Gene set enrichment for two or three categories
getTable | Class '"concub"'
getTable-method | Class '"concub"'
GO2level | Filter GO and KEGG database
GO2list | Filter GO and KEGG database
GO2offspring | Filter GO and KEGG database
initialize-method | Class '"concub"'
initialize-method | Class '"concubfilter"'
intersectPresort | Optimized operations of sets of character-vectors
KEGG2list | Filter GO and KEGG database
marioni | Affymetrix microarray gene expression data
minimum.l2or | Class '"concubfilter"'
minimum.l2or-method | Class '"concubfilter"'
minimum.l2or<- | Class '"concubfilter"'
minimum.l2or<--method | Class '"concubfilter"'
p.value | Class '"concubfilter"'
p.value-method | Class '"concubfilter"'
p.value<- | Class '"concubfilter"'
p.value<--method | Class '"concubfilter"'
plotConCub | Generate a heatmap showing log2 odds ratios and P-values.
pval2star | Transform P-values to stars
runConCub | Enrichment analysis on two- or three-way contingency tables.
setdiffPresort | Optimized operations of sets of character-vectors
show-method | Class '"concub"'
show-method | Class '"concubfilter"'
skip.min.group | Class '"concubfilter"'
skip.min.group-method | Class '"concubfilter"'
skip.min.group<- | Class '"concubfilter"'
skip.min.group<--method | Class '"concubfilter"'
skip.min.obs | Class '"concubfilter"'
skip.min.obs-method | Class '"concubfilter"'
skip.min.obs<- | Class '"concubfilter"'
skip.min.obs<--method | Class '"concubfilter"'
skip.zeroobs | Class '"concubfilter"'
skip.zeroobs-method | Class '"concubfilter"'
skip.zeroobs<- | Class '"concubfilter"'
skip.zeroobs<--method | Class '"concubfilter"'
sortAscii | Optimized operations of sets of character-vectors
test.direction | Class '"concubfilter"'
test.direction-method | Class '"concubfilter"'
test.direction<- | Class '"concubfilter"'
test.direction<--method | Class '"concubfilter"'