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

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.

AuthorKevin R. Coombes
Date of publication2016-05-09 20:45:21
MaintainerKevin R. Coombes <krc@silicovore.com>
LicenseApache License (== 2.0)
Version3.1.3
http://oompa.r-forge.r-project.org/

View on R-Forge

Functions

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
Bum Man page
Bum-class Man page
BumSummary Man page
BumSummary-class Man page
countSignificant Man page
countSignificant,ANY-method Man page
countSignificant,Bum-method Man page
countSignificant,Dudoit-method Man page
countSignificant-method Man page
countSignificant,MultiWilcoxonTest-method Man page
countSignificant,Sam-method Man page
countSignificant,TNoM-method Man page
cutoffSignificant Man page
cutoffSignificant,ANY-method Man page
cutoffSignificant,Bum-method Man page
cutoffSignificant,Dudoit-method Man page
cutoffSignificant-method Man page
cutoffSignificant,MultiWilcoxonTest-method Man page
Dudoit Man page
Dudoit-class Man page
dwil Man page
fullTNoM-class Man page
hist,Bum-method Man page
hist,fullTNoM-method Man page
hist,MultiLinearModel-method Man page
hist,MultiTtest-method Man page
hist,MultiWilcoxonTest-method Man page
image,Bum-method Man page
likelihoodBum Man page
MultiLinearModel Man page
MultiLinearModel-class Man page
MultiTtest Man page
MultiTtest-class Man page
MultiTtestPaired Man page
MultiTtestPaired-class Man page
MultiTtestUnequal Man page
MultiTtestUnequal-class Man page
multiTukey Man page
MultiWilcoxonTest Man page
MultiWilcoxonTest-class Man page
plot,Dudoit,missing-method Man page
plot,fullTNoM,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
print,SingleGroup-method Man page
print,TwoGroupStats-method Man page
rankSum Man page
Sam Man page
Sam-class Man page
SamSummary Man page
SamSummary-class Man page
selectSignificant Man page
selectSignificant,ANY-method Man page
selectSignificant,Bum-method Man page
selectSignificant,Dudoit-method Man page
selectSignificant-method Man page
selectSignificant,MultiWilcoxonTest-method Man page
selectSignificant,Sam-method Man page
selectSignificant,TNoM-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
SingleGroup Man page
SingleGroup-class Man page
SmoothTtest Man page
SmoothTtest-class Man page
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
TNoM Man page
TNoM-class Man page
TNoMSummary Man page
TNoMSummary-class Man page
TwoGroupStats Man page
TwoGroupStats-class Man page
update,TNoM-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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