Pairwise INTegration of functional genomics data


[Up] [Top]

Documentation for package ‘pint’ version 1.36.0

Help Pages

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"