ClassComparison: Classes and Methods for "Class Comparison" Problems on Microarrays
Version 3.1.4

The ClassComparison package defines the classes used for "class comparison" problems in the OOMPA project. Class comparison includes tests for differential expression; see Simon's book for details on typical problem types.

Browse man pages Browse package API and functions Browse package files

AuthorKevin R. Coombes
Bioconductor views DifferentialExpression Microarray MultipleComparisons
Date of publication2017-04-25 13:41:44
MaintainerKevin R. Coombes <krc@silicovore.com>
LicenseApache License (== 2.0)
Version3.1.4
URL http://oompa.r-forge.r-project.org/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("ClassComparison", repos="http://R-Forge.R-project.org")

Man pages

cc00-0-Bum-class: Class "Bum"
cc00-1-BumSummary-class: Class "BumSummary"
cc00-2-significant-method: Generic Methods for Significance
cc01-0-MultiTtest-class: Class "MultiTtest"
cc01-1-variantT-class: Classes for Variant T-tests
cc02-0-MultiWilcoxonTest-class: Class "MultiWilcoxonTest"
cc02-1-dwil: Wilcoxon Density Function
cc02-2-rankSum: Wilcoxon Rank-Sum Statistic
cc03-0-MultiLinearModel-class: Class "MultiLinearModel"
cc04-0-Dudoit-class: Class "Dudoit"
cc05-0-TNoM-class: Classes "TNoM" and "fullTNoM"
cc05-1-TNoMSummary-class: Class "TNoMSummary"
cc06-0-Sam-class: Class "Sam"
cc06-1-SamSummary-class: Class "SamSummary"
cc07-0-TwoGroupStats-class: Class "TwoGroupStats"
cc08-0-SingleGroup-class: Class "SingleGroup"
cc09-0-SmoothTtest-class: Class "SmoothTtest"

Functions

Bum Man page Source code
Bum-class Man page
BumSummary Man page
BumSummary-class Man page
Dudoit Man page Source code
Dudoit-class Man page
MultiLinearModel Man page Source code
MultiLinearModel-class Man page
MultiTtest Man page Source code
MultiTtest-class Man page
MultiTtestPaired Man page Source code
MultiTtestPaired-class Man page
MultiTtestUnequal Man page Source code
MultiTtestUnequal-class Man page
MultiWilcoxonTest Man page Source code
MultiWilcoxonTest-class Man page
Sam Man page Source code
Sam-class Man page
SamSummary Man page
SamSummary-class Man page
SingleGroup Man page Source code
SingleGroup-class Man page
SmoothTtest Man page Source code
SmoothTtest-class Man page
TNoM Man page Source code
TNoM-class Man page
TNoMSummary Man page
TNoMSummary-class Man page
TwoGroupStats Man page Source code
TwoGroupStats-class Man page
anova,MultiLinearModel-method Man page
as.data.frame,MultiTtest-method Man page
as.data.frame,SingleGroup-method Man page
as.data.frame,SmoothTtest-method Man page
as.data.frame,TwoGroupStats-method Man page
compute.score Source code
countSignificant Man page
countSignificant,ANY-method Man page
countSignificant,Bum-method Man page
countSignificant,Dudoit-method Man page
countSignificant,MultiWilcoxonTest-method Man page
countSignificant,Sam-method Man page
countSignificant,TNoM-method Man page
countSignificant-method Man page
cutoffByEB Source code
cutoffByFDR Source code
cutoffSignificant Man page
cutoffSignificant,ANY-method Man page
cutoffSignificant,Bum-method Man page
cutoffSignificant,Dudoit-method Man page
cutoffSignificant,MultiWilcoxonTest-method Man page
cutoffSignificant-method Man page
dwil Man page Source code
ea Source code
fullTNoM-class Man page
group.coding Source code
hist,Bum-method Man page
hist,MultiLinearModel-method Man page
hist,MultiTtest-method Man page
hist,MultiWilcoxonTest-method Man page
hist,fullTNoM-method Man page
image,Bum-method Man page
likelihoodBum Man page Source code
lo.front Source code
lo.sho Source code
lp Source code
merge Source code
multiTukey Man page Source code
plot,Dudoit,missing-method Man page
plot,MultiLinearModel,ANY-method Man page
plot,MultiLinearModel,missing-method Man page
plot,MultiTtest,ANY-method Man page
plot,MultiTtest,missing-method Man page
plot,MultiWilcoxonTest,missing-method Man page
plot,Sam,missing-method Man page
plot,SingleGroup,missing-method Man page
plot,SmoothTtest,missing-method Man page
plot,TwoGroupStats,missing-method Man page
plot,fullTNoM,missing-method Man page
pounds Source code
print,SingleGroup-method Man page
print,TwoGroupStats-method Man page
probDiff Source code
rankSum Man page Source code
scored.coding Source code
scramble.samples.TNoM Source code
screwyPlot Source code
selectSignificant Man page
selectSignificant,ANY-method Man page
selectSignificant,Bum-method Man page
selectSignificant,Dudoit-method Man page
selectSignificant,MultiWilcoxonTest-method Man page
selectSignificant,Sam-method Man page
selectSignificant,TNoM-method Man page
selectSignificant-method Man page
show,BumSummary-method Man page
show,SamSummary-method Man page
show,SingleGroup-method Man page
show,TNoMSummary-method Man page
show,TwoGroupStats-method Man page
simulate.genes.TNoM Source code
smu Source code
summary,Bum-method Man page
summary,MultiLinearModel-method Man page
summary,MultiTtest-method Man page
summary,MultiTtestPaired-method Man page
summary,MultiTtestUnequal-method Man page
summary,MultiWilcoxonTest-method Man page
summary,Sam-method Man page
summary,SingleGroup-method Man page
summary,SmoothTtest-method Man page
summary,TNoM-method Man page
summary,TwoGroupStats-method Man page
update,TNoM-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/cc00-bum.R
R/cc01-ttest.R
R/cc02-EfronTibshirani.R
R/cc03-fastlm.R
R/cc04-Dudoit.R
R/cc05-tnom.R
R/cc06-Sam.R
R/cc07-twoGroupStats.R
R/cc08-singleGroup.R
R/cc09-smoothT.R
R/cc10-pairedT.R
TODO
build
build/vignette.rds
inst
inst/doc
inst/doc/oompa-cc.R
inst/doc/oompa-cc.Rnw
inst/doc/oompa-cc.pdf
inst/samples
inst/samples/exprSet-example.R
inst/samples/test00-BUM.R
inst/samples/test01-ttest.R
inst/samples/test02-eb.R
inst/samples/test03-lm.R
inst/samples/test04-dudoit.R
inst/samples/test05-tnom.R
inst/samples/test06-sam.R
inst/samples/test07-twoGroupStats.R
inst/samples/test08-singleGroup.R
inst/samples/test09-smoothT.R
inst/samples/test10-Tvariant.R
man
man/cc00-0-Bum-class.Rd
man/cc00-1-BumSummary-class.Rd
man/cc00-2-significant-method.Rd
man/cc01-0-MultiTtest-class.Rd
man/cc01-1-variantT-class.Rd
man/cc02-0-MultiWilcoxonTest-class.Rd
man/cc02-1-dwil.Rd
man/cc02-2-rankSum.Rd
man/cc03-0-MultiLinearModel-class.Rd
man/cc04-0-Dudoit-class.Rd
man/cc05-0-TNoM-class.Rd
man/cc05-1-TNoMSummary-class.Rd
man/cc06-0-Sam-class.Rd
man/cc06-1-SamSummary-class.Rd
man/cc07-0-TwoGroupStats-class.Rd
man/cc08-0-SingleGroup-class.Rd
man/cc09-0-SmoothTtest-class.Rd
tests
tests/testBum.R
tests/testBum.Rout.save
tests/testDiff.R
tests/testDiff.Rout.save
vignettes
vignettes/oompa-cc.Rnw
ClassComparison documentation built on May 21, 2017, 12:15 a.m.