Pairwise INTegration of functional genomics data


[Up] [Top]

Documentation for package ‘pint’ version 1.2.0

Help Pages

C D F G I O P S T W Z misc

-- C --

ChromosomeArmModels-class Class "ChromosomeArmModels", for dependency models in chromosomal arm
ChromosomeModels-class Class "ChromosomeModels"

-- D --

dependency score plotting Dependency score plotting
DependencyModel-class Class "DependencyModel"

-- F --

findModel Class "ChromosomeArmModels", for dependency models in chromosomal arm
findModel-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
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.
fit.dependency.model Fit dependency model between two data sets.
fixed.window Form data with a selected window size for the model fitting

-- G --

geneCopyNum Gene copy number data in chromosome 17
geneExp Gene expression data in chromosome 17
GenomeModels-class Class "GenomeModels"
getArm Class "ChromosomeArmModels", for dependency models in chromosomal arm
getArm-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
getArm-method Class "DependencyModel"
getChromosome Class "ChromosomeArmModels", for dependency models in chromosomal arm
getChromosome-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
getChromosome-method Class "ChromosomeModels"
getChromosome-method Class "DependencyModel"
getGeneName Class "DependencyModel"
getGeneName-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
getGeneName-method Class "DependencyModel"
getLoc Class "DependencyModel"
getLoc-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
getLoc-method Class "DependencyModel"
getModelMethod Class "ChromosomeArmModels", for dependency models in chromosomal arm
getModelMethod-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
getModelMethod-method Class "ChromosomeModels"
getModelMethod-method Class "DependencyModel"
getModelMethod-method Class "GenomeModels"
getModelNumbers Class "ChromosomeArmModels", for dependency models in chromosomal arm
getModelNumbers-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
getParams Class "ChromosomeArmModels", for dependency models in chromosomal arm
getParams-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
getParams-method Class "ChromosomeModels"
getParams-method Class "DependencyModel"
getParams-method Class "GenomeModels"
getPArm Class "ChromosomeModels"
getPArm-method Class "ChromosomeModels"
getPhi Class "DependencyModel"
getPhi-method Class "DependencyModel"
getQArm Class "ChromosomeModels"
getQArm-method Class "ChromosomeModels"
getScore Class "DependencyModel"
getScore-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
getScore-method Class "DependencyModel"
getW Class "DependencyModel"
getW-method Class "DependencyModel"
getWindowSize Class "ChromosomeArmModels", for dependency models in chromosomal arm
getWindowSize-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
getWindowSize-method Class "ChromosomeModels"
getWindowSize-method Class "DependencyModel"
getWindowSize-method Class "GenomeModels"

-- I --

isEmpty Class "ChromosomeArmModels", for dependency models in chromosomal arm
isEmpty-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
isEmpty-method Class "ChromosomeModels"
iterative.window Form data with a selected window size for the model fitting

-- O --

orderGenes Class "ChromosomeArmModels", for dependency models in chromosomal arm
orderGenes-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
orderGenes-method Class "ChromosomeModels"
orderGenes-method Class "GenomeModels"

-- P --

pcca Fit dependency model between two data sets.
pcca.isotropic Fit dependency model between two data sets.
pfa Fit dependency model between two data sets.
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.ChromosomeArmModels Dependency score plotting
plot.ChromosomeModels Dependency score plotting
plot.DependencyModel Dependency score plotting
plot.GenomeModels Dependency score plotting
ppca Fit dependency model between two data sets.

-- S --

screen.cgh.mir Fits dependency models to chromosomal arm, chromosome or the whole
screen.cgh.mrna Fits dependency models to chromosomal arm, chromosome or the whole
setArm<- Class "DependencyModel"
setArm<--method Class "DependencyModel"
setChromosome<- Class "DependencyModel"
setChromosome<--method Class "DependencyModel"
setGeneName<- Class "DependencyModel"
setGeneName<--method Class "DependencyModel"
setLoc<- Class "DependencyModel"
setLoc<--method Class "DependencyModel"
sparse.window Form data with a selected window size for the model fitting

-- T --

topGenes Class "ChromosomeArmModels", for dependency models in chromosomal arm
topGenes-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
topGenes-method Class "ChromosomeModels"
topGenes-method Class "GenomeModels"
topModels Class "ChromosomeArmModels", for dependency models in chromosomal arm
topModels-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
topModels-method Class "ChromosomeModels"
topModels-method Class "GenomeModels"

-- W --

W.effects The model parameters z and W

-- Z --

z.effects The model parameters z and W
z.expectation The model parameters z and W

-- misc --

[[ Class "ChromosomeArmModels", for dependency models in chromosomal arm
[[-method Class "ChromosomeArmModels", for dependency models in chromosomal arm
[[-method Class "GenomeModels"
[[<- Class "ChromosomeArmModels", for dependency models in chromosomal arm
[[<--method Class "ChromosomeArmModels", for dependency models in chromosomal arm
[[<--method Class "GenomeModels"