Introduction | Getting Started | Gene-by-gene t-tests | Beta-uniform mixture models to account for multiple testing | Wilcoxon rank sum tests and empirical Bayes | Permutation based methods | Significance Analysis of Microarrays | Other class comparison approaches
Package: ClassComparison 3.3.5
Kevin R. Coombes
ClassComparison: Classes and Methods for "Class Comparison" Problems on Microarrays
Defines the classes used for "class comparison" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class comparison includes tests for differential expression; see Simon's book for details on typical problem types.
Authors:
ClassComparison_3.3.5.tar.gz
ClassComparison_3.3.5.zip(r-4.7)ClassComparison_3.3.5.zip(r-4.6)ClassComparison_3.3.5.zip(r-4.5)
ClassComparison_3.3.5.tgz(r-4.6-any)ClassComparison_3.3.5.tgz(r-4.5-any)
ClassComparison_3.3.5.tar.gz(r-4.7-any)ClassComparison_3.3.5.tar.gz(r-4.6-any)
ClassComparison_3.3.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ClassComparison/json (API)
| # Install 'ClassComparison' in R: |
| install.packages('ClassComparison', repos = c('https://r-forge.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://r-forge.r-project.org/projects/oompa
microarraydifferentialexpressionmultiplecomparisons
Last updated from:969e77c656. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 165 | ||
| source / vignettes | OK | 169 | ||
| linux-release-x86_64 | OK | 157 | ||
| macos-release-arm64 | OK | 74 | ||
| macos-oldrel-arm64 | OK | 119 | ||
| windows-devel | OK | 82 | ||
| windows-release | OK | 101 | ||
| windows-oldrel | OK | 75 | ||
| wasm-release | OK | 111 |
Exports:anovaas.data.frameBumcountSignificantcutoffSignificantDudoitdwilhistimagelikelihoodBumMultiLinearModelMultiTtestMultiTtestPairedMultiTtestUnequalmultiTukeyMultiWilcoxonTestplotprobDiffrankSumSamselectSignificantshowSingleGroupSmoothTtestsummaryTNoMTwoGroupStatsupdate
Dependencies:BiobaseBiocGenericsclustergenericsoompaBase
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Class "Bum" | Bum Bum-class countSignificant,Bum-method cutoffSignificant,Bum-method hist,Bum-method image,Bum-method likelihoodBum selectSignificant,Bum-method summary,Bum-method |
| Class "BumSummary" | BumSummary BumSummary-class show,BumSummary-method |
| Class "Dudoit" | countSignificant,Dudoit-method cutoffSignificant,Dudoit-method Dudoit Dudoit-class plot,Dudoit,missing-method selectSignificant,Dudoit-method |
| Wilcoxon Density Function | dwil |
| Class "MultiLinearModel" | anova,MultiLinearModel-method as.data.frame,MultiLinearModel-method hist,MultiLinearModel-method MultiLinearModel MultiLinearModel-class multiTukey plot,MultiLinearModel,ANY-method plot,MultiLinearModel,missing-method summary,MultiLinearModel-method |
| Class "MultiTtest" | as.data.frame,MultiTtest-method hist,MultiTtest-method MultiTtest MultiTtest-class plot,MultiTtest,ANY-method plot,MultiTtest,missing-method summary,MultiTtest-method |
| Class "MultiWilcoxonTest" | countSignificant,MultiWilcoxonTest-method cutoffSignificant,MultiWilcoxonTest-method hist,MultiWilcoxonTest-method MultiWilcoxonTest MultiWilcoxonTest-class plot,MultiWilcoxonTest,missing-method probDiff,MultiWilcoxonTest-method selectSignificant,MultiWilcoxonTest-method summary,MultiWilcoxonTest-method |
| Wilcoxon Rank-Sum Statistic | rankSum |
| Class "Sam" | countSignificant,Sam-method plot,Sam,missing-method Sam Sam-class selectSignificant,Sam-method summary,Sam-method |
| Class "SamSummary" | SamSummary SamSummary-class show,SamSummary-method |
| Generic Methods for Significance | countSignificant countSignificant,ANY-method countSignificant-method cutoffSignificant cutoffSignificant,ANY-method cutoffSignificant-method probDiff probDiff,ANY-method probDiff-method selectSignificant selectSignificant,ANY-method selectSignificant-method |
| Class "SingleGroup" | as.data.frame,SingleGroup-method plot,SingleGroup,missing-method print,SingleGroup-method show,SingleGroup-method SingleGroup SingleGroup-class summary,SingleGroup-method |
| Class "SmoothTtest" | as.data.frame,SmoothTtest-method plot,SmoothTtest,missing-method SmoothTtest SmoothTtest-class summary,SmoothTtest-method |
| Classes "TNoM" and "fullTNoM" | countSignificant,TNoM-method fullTNoM-class hist,fullTNoM-method plot,fullTNoM,missing-method selectSignificant,TNoM-method summary,TNoM-method TNoM TNoM-class update,TNoM-method |
| Class "TNoMSummary" | show,TNoMSummary-method TNoMSummary TNoMSummary-class |
| Class "TwoGroupStats" | as.data.frame,TwoGroupStats-method plot,TwoGroupStats,missing-method print,TwoGroupStats-method show,TwoGroupStats-method summary,TwoGroupStats-method TwoGroupStats TwoGroupStats-class |
| Classes for Variant T-tests | MultiTtestPaired MultiTtestPaired-class MultiTtestUnequal MultiTtestUnequal-class summary,MultiTtestPaired-method summary,MultiTtestUnequal-method |