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| alias,gt.object-method | Class "gt.object" for storing the result of the function gt |
| alias<- | Class "gt.object" for storing the result of the function gt |
| alias<-,gt.object-method | Class "gt.object" for storing the result of the function gt |
| annotation.vandeVijver | Some selected annotations for the breast cancer data from Rosetta Inpharmatics LLC and Netherlands Cancer Institute, to serve as example data in the globaltest package. (Deprecated) |
| checkerboard | Checkerboard plot for Global Test (Deprecated) |
| coefficients,mlogit-method | Multinomial Logistic Regression |
| combine,gt.result,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| comparative | Comparative proportions for the Global Test |
| covariates | Global Test diagnostic plots |
| diagnostics | Global Test diagnostic plots |
| draw | Multiple testing correction for the Global Test |
| features | Global Test diagnostic plots |
| findFocus | Multiple testing correction for the Global Test |
| fit | Class "gt.result" for results of the function globaltest (Deprecated) |
| fit,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| fitted.values,mlogit-method | Multinomial Logistic Regression |
| focusLevel | Multiple testing correction for the Global Test |
| geneplot | Gene Plot for Global Test (Deprecated) |
| genesets | Class "gt.result" for results of the function globaltest (Deprecated) |
| genesets,GOstructure-method | Class "GOstructure" (Deprecated) |
| getFocus | Multiple testing on the GO graph (Deprecated) |
| globaltest | Global Test (Deprecated) |
| GOstructure | Class "GOstructure" (Deprecated) |
| GOstructure-class | Class "GOstructure" (Deprecated) |
| gt | Global Test (new implementation, 2009) |
| gt.barplot | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| gt.barplot-class | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| gt.multtest | Correct globaltest results for multiple testing (Deprecated) |
| gt.object | Class "gt.object" for storing the result of the function gt |
| gt.object-class | Class "gt.object" for storing the result of the function gt |
| gt.options | Options for globaltest package |
| gt.result | Class "gt.result" for results of the function globaltest (Deprecated) |
| gt.result-class | Class "gt.result" for results of the function globaltest (Deprecated) |
| gtBroad | Gene set testing of gene set databases using Global Test |
| gtGO | Gene set testing of gene set databases using Global Test |
| gtKEGG | Gene set testing of gene set databases using Global Test |
| hist,gt.object-method | Class "gt.object" for storing the result of the function gt |
| hist,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| inheritance | Multiple testing correction for the Global Test |
| leafNodes | Multiple testing correction for the Global Test |
| length,GOstructure-method | Class "GOstructure" (Deprecated) |
| length,gt.barplot-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| length,gt.object-method | Class "gt.object" for storing the result of the function gt |
| length,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| makeGOstructure | Multiple testing on the GO graph (Deprecated) |
| mlogit | Multinomial Logistic Regression |
| mlogit-class | Multinomial Logistic Regression |
| model.matrix,gt.object-method | Class "gt.object" for storing the result of the function gt |
| names,gt.barplot-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| names,gt.object-method | Class "gt.object" for storing the result of the function gt |
| names,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| names<-,gt.barplot-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| names<-,gt.object-method | Class "gt.object" for storing the result of the function gt |
| names<-,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| p.adjust,gt.object-method | Class "gt.object" for storing the result of the function gt |
| p.value | Class "gt.object" for storing the result of the function gt |
| p.value,gt.object-method | Class "gt.object" for storing the result of the function gt |
| p.value,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| permutations | Permutations version of the Global Test (Deprecated) |
| plot,gt.barplot-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| regressionplot | Regression Plot for Global Test (Deprecated) |
| residuals,mlogit-method | Multinomial Logistic Regression |
| result | Class "gt.object" for storing the result of the function gt |
| result,gt.barplot-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| result,gt.object-method | Class "gt.object" for storing the result of the function gt |
| result,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| sampleplot | Sample Plot for Global Test (Deprecated) |
| sampling | Sampling random 'pathways' for the Global Test |
| scale,gt.barplot-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| show,GOstructure-method | Class "GOstructure" (Deprecated) |
| show,gt.barplot-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| show,gt.object-method | Class "gt.object" for storing the result of the function gt |
| show,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| show,mlogit-method | Multinomial Logistic Regression |
| size | Class "gt.object" for storing the result of the function gt |
| size,gt.object-method | Class "gt.object" for storing the result of the function gt |
| size,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| sort,gt.barplot-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| sort,gt.object-method | Class "gt.object" for storing the result of the function gt |
| sort,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| subjects | Global Test diagnostic plots |
| subsets | Class "gt.object" for storing the result of the function gt |
| subsets,gt.object-method | Class "gt.object" for storing the result of the function gt |
| summary,gt.object-method | Class "gt.object" for storing the result of the function gt |
| summary,mlogit-method | Multinomial Logistic Regression |
| vandeVijver | A subset of the Breast cancer data from Rosetta Inpharmatics LLC and Netherlands Cancer Institute. (Deprecated) |
| weights,gt.object-method | Class "gt.object" for storing the result of the function gt |
| z.score | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| z.score,gt.barplot-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| z.score,gt.object-method | Class "gt.object" for storing the result of the function gt |
| z.score,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| [,gt.barplot-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated) |
| [,gt.object-method | Class "gt.object" for storing the result of the function gt |
| [,gt.result-method | Class "gt.result" for results of the function globaltest (Deprecated) |
| [[,gt.object-method | Class "gt.object" for storing the result of the function gt |