geecc: Gene Set Enrichment Analysis Extended to Contingency Cubes
Version 1.10.0

Use log-linear models to perform hypergeometric and chi-squared tests for gene set enrichments for two (based on contingency tables) or three categories (contingency cubes). Categories can be differentially expressed genes, GO terms, sequence length, GC content, chromosomal position, phylostrata, divergence-strata, ....

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AuthorMarkus Boenn
Bioconductor views BiologicalQuestion GO GeneExpression GeneSetEnrichment Microarray RNASeq StatisticalMethod Transcription WorkflowStep
Date of publicationNone
MaintainerMarkus Boenn <markus.boenn@ufz.de>
LicenseGPL (>= 2)
Version1.10.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("geecc")

Man pages

concub-class: Class '"concub"'
concubfilter-class: Class '"concubfilter"'
filterConCub: Filter results from two- or three-way tests
geecc-package: Gene set enrichment for two or three categories
GO2list: Filter GO and KEGG database
marioni: Affymetrix microarray gene expression data
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.
setop: Optimized operations of sets of character-vectors

Functions

GO2level Man page Source code
GO2list Man page Source code
GO2offspring Man page Source code
KEGG2list Man page Source code
cf_intersect6 Source code
cf_setdiff1 Source code
cf_special1 Source code
checkFormula Source code
concub-class Man page
concubfilter-class Man page
drop.insignif.layer Man page
drop.insignif.layer,concubfilter-method Man page
drop.insignif.layer<- Man page
drop.insignif.layer<-,concubfilter-method Man page
drop.lowl2or.layer Man page
drop.lowl2or.layer,concubfilter-method Man page
drop.lowl2or.layer<- Man page
drop.lowl2or.layer<-,concubfilter-method Man page
drop.wrongdir.layer Man page
drop.wrongdir.layer,concubfilter-method Man page
drop.wrongdir.layer<- Man page
drop.wrongdir.layer<-,concubfilter-method Man page
filterConCub Man page Source code
filter_drop.insignif.layer Source code
filter_drop.lowl2or.layer Source code
filter_drop.wrongdir.layer Source code
filter_dropLayer Source code
geecc Man page
geecc-package Man page
getContingencyCube Source code
getContingencyTable Source code
getItemsInEachCategory Source code
getLoadedList Source code
getNamesOfEachCategory Source code
getNumberOfFactorLevels Source code
getOptOfCategory Source code
getTable Man page
getTable,concub-method Man page
getTypeOf_transformTable Source code
get_gochildren Source code
haszerodim Source code
initialize,concub-method Man page
initialize,concubfilter-method Man page
intersectPresort Man page Source code
keepLayer Source code
loglinmodel Source code
marioni Man page
minimum.l2or Man page
minimum.l2or,concubfilter-method Man page
minimum.l2or<- Man page
minimum.l2or<-,concubfilter-method Man page
my_separator Source code
onAttach Source code
onUnload Source code
p.value Man page
p.value,concubfilter-method Man page
p.value<- Man page
p.value<-,concubfilter-method Man page
performTest Source code
performTest_approx Source code
plotConCub Man page Source code
pval2star Man page Source code
rcpp_hello_world Source code
runConCub Man page Source code
setdiffPresort Man page Source code
show,concub-method Man page
show,concubfilter-method Man page
skip.min.group Man page
skip.min.group,concubfilter-method Man page
skip.min.group<- Man page
skip.min.group<-,concubfilter-method Man page
skip.min.obs Man page
skip.min.obs,concubfilter-method Man page
skip.min.obs<- Man page
skip.min.obs<-,concubfilter-method Man page
skip.zeroobs Man page
skip.zeroobs,concubfilter-method Man page
skip.zeroobs<- Man page
skip.zeroobs<-,concubfilter-method Man page
sortAscii Man page Source code
special1 Source code
test.direction Man page
test.direction,concubfilter-method Man page
test.direction<- Man page
test.direction<-,concubfilter-method Man page
transformTable Source code
translate Source code

Files

DESCRIPTION
NAMESPACE
R
R/RcppExports.R
R/concub-class.R
R/concubfilter-class.R
R/geecc.R
R/littlehelpers.R
R/zzz.R
build
build/vignette.rds
data
data/datalist
data/marioni.rda
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/geecc.R
inst/doc/geecc.Rnw
inst/doc/geecc.pdf
man
man/GO2list.Rd
man/concub-class.Rd
man/concubfilter-class.Rd
man/filterConCub.Rd
man/geecc-package.Rd
man/marioni.Rd
man/plotConCub.Rd
man/pval2star.Rd
man/runConCub.Rd
man/setop.Rd
src
src/RcppExports.cpp
src/rcpp_hello_world.cpp
src/specialists.cpp
vignettes
vignettes/geecc.Rnw
vignettes/geecc.bib
geecc documentation built on May 20, 2017, 9:57 p.m.