Gene set Enrichment analysis Extended to Contingency Cubes


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Documentation for package ‘geecc’ version 1.4.0

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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"'
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.
runConCub Enrichment analysis on two- or three-way contingency tables.
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"'
test.direction Class '"concubfilter"'
test.direction-method Class '"concubfilter"'
test.direction<- Class '"concubfilter"'
test.direction<--method Class '"concubfilter"'