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" |