| as.data.frame-method | Class "ChromosomeModels" |
| as.data.frame-method | Class "GenomeModels" |
| ChromosomeModels-class | Class "ChromosomeModels" |
| dependency score plotting | Dependency score plotting |
| findModel | Class "ChromosomeModels" |
| findModel-method | Class "ChromosomeModels" |
| findModel-method | Class "GenomeModels" |
| fit.byname | Fit dependency model around one gene between two data sets. |
| fit.cgh.mir.byname | Fit dependency model around one gene between two data sets. |
| fit.cgh.mrna.byname | Fit dependency model around one gene between two data sets. |
| fixed.window | Form data with a selected window size for the model fitting |
| geneCopyNum | Gene copy number data in chromosome 17 |
| GeneDependencyModel-class | Class "GeneDependencyModel" |
| geneExp | Gene expression data in chromosome 17 |
| GenomeModels-class | Class "GenomeModels" |
| get.neighboring.probes | Get neighboring probes |
| get.neighs | get.neighs |
| getArm | Class "ChromosomeModels" |
| getArm-method | Class "ChromosomeModels" |
| getArm-method | Class "GeneDependencyModel" |
| getChromosome | Class "ChromosomeModels" |
| getChromosome-method | Class "ChromosomeModels" |
| getChromosome-method | Class "GeneDependencyModel" |
| getGeneName | Class "ChromosomeModels" |
| getGeneName-method | Class "ChromosomeModels" |
| getGeneName-method | Class "GeneDependencyModel" |
| getLoc | Class "GeneDependencyModel" |
| getLoc-method | Class "ChromosomeModels" |
| getLoc-method | Class "GeneDependencyModel" |
| getModelMethod | Class "ChromosomeModels" |
| getModelMethod-method | Class "ChromosomeModels" |
| getModelMethod-method | Class "GenomeModels" |
| getModelNumbers | Class "ChromosomeModels" |
| getModelNumbers-method | Class "ChromosomeModels" |
| getModelNumbers-method | Class "GenomeModels" |
| getParams | Class "ChromosomeModels" |
| getParams-method | Class "ChromosomeModels" |
| getParams-method | Class "GenomeModels" |
| getPArm | Class "ChromosomeModels" |
| getPArm-method | Class "ChromosomeModels" |
| getQArm | Class "ChromosomeModels" |
| getQArm-method | Class "ChromosomeModels" |
| getScore | Class "GeneDependencyModel" |
| getScore-method | Class "ChromosomeModels" |
| getScore-method | Class "GeneDependencyModel" |
| getWindowSize | Class "ChromosomeModels" |
| getWindowSize-method | Class "ChromosomeModels" |
| getWindowSize-method | Class "GeneDependencyModel" |
| getWindowSize-method | Class "GenomeModels" |
| getZ-method | Class "GeneDependencyModel" |
| isEmpty | Class "ChromosomeModels" |
| isEmpty-method | Class "ChromosomeModels" |
| iterative.window | Form data with a selected window size for the model fitting |
| join.top.regions | Merge the overlapping top chromosomal regions. |
| order.feature.info | Order the gene information table by chromosomal locations. |
| orderGenes | Class "ChromosomeModels" |
| orderGenes-method | Class "ChromosomeModels" |
| orderGenes-method | Class "GenomeModels" |
| pint.data | Forms a data set and pairs samples in two data sets. |
| pint.match | Forms a data set and pairs samples in two data sets. |
| plot.ChromosomeModels | Dependency score plotting |
| plot.GeneDependencyModel | Dependency score plotting |
| plot.GenomeModels | Dependency score plotting |
| screen.cgh.mir | Fits dependency models to chromosomal arm, chromosome or the whole genome. |
| screen.cgh.mrna | Fits dependency models to chromosomal arm, chromosome or the whole genome. |
| setArm<- | Class "GeneDependencyModel" |
| setArm<--method | Class "GeneDependencyModel" |
| setChromosome<- | Class "GeneDependencyModel" |
| setChromosome<--method | Class "GeneDependencyModel" |
| setGeneName<- | Class "GeneDependencyModel" |
| setGeneName<--method | Class "GeneDependencyModel" |
| setLoc<- | Class "GeneDependencyModel" |
| setLoc<--method | Class "GeneDependencyModel" |
| sparse.window | Form data with a selected window size for the model fitting |
| summarize.region.parameters | Summarize overlapping models. |
| topGenes | Class "ChromosomeModels" |
| topGenes-method | Class "ChromosomeModels" |
| topGenes-method | Class "GenomeModels" |
| topModels | Class "ChromosomeModels" |
| topModels-method | Class "ChromosomeModels" |
| topModels-method | Class "GenomeModels" |
| W.effects | The model parameters z and W |
| z.effects | The model parameters z and W |
| [[ | Class "ChromosomeModels" |
| [[-method | Class "ChromosomeModels" |
| [[-method | Class "GenomeModels" |
| [[<- | Class "ChromosomeModels" |
| [[<--method | Class "ChromosomeModels" |
| [[<--method | Class "GenomeModels" |