GeneDependencyModel-class: Class "GeneDependencyModel"

In pint: Pairwise INTegration of functional genomics data

Description

A Genomic Dependency model for two data sets

Objects from the Class

Used to represent individual dependency models for screening inside ChromosomeModels.

Slots

loc

middle location of the window in base pairs

geneName

name of the gene in the middle of the window

chromosome

Chromosome where the dependency model is calculated

arm

Chromosome arm where the dependency model is calculated

W

a list of X, Y and total components containing the relationship between two data sets; for dependency model for one dataset, only total is given

phi

a list of X, Y and total components containing the data set specific covariances; for dependency model for one dataset, only total is given

score

score for fitness of model

method

name of the used method

params

list of parameters used in dependency model

data

The data used to calculate the dependency model

z

The latent variable Z

Extends

Class DependencyModel directly.

Methods

setLoc<-

signature(model = "GeneDependencyModel"): sets models location

setGeneName<-

signature(model = "GeneDependencyModel"): sets models gene name

setChromosome<-

signature(model = "GeneDependencyModel"): sets models chromosome

setArm<-

signature(model = "GeneDependencyModel"): sets models chromosome arm

getLoc

signature(model = "GeneDependencyModel"): Returns the middle location of the window

getGeneName

signature(model = "GeneDependencyModel"): Returns the name of the gene in the middle of window

getChromosome

signature(model = "GeneDependencyModel"): Returns the chromosome

getArm

signature(model = "GeneDependencyModel"): Returns the chromosome arm

getWindowSize

signature(model = "GeneDependencyModel"): Returns the size of window

getZ

signature(model = "GeneDependencyModel"): Calculates the expectation of latent variable Z. The original data is needed as arguments as given to screen function

Author(s)

Olli-Pekka Huovilainen [e-mail]

See Also

For calculation of dependency models for chromosomal arm, chromosome or genome: screen.cgh.mrna. Dependency models for whole chromosome: ChromosomeModels. Dependency models for whole genome: GenomeModels. For plotting dependency scores see dependency score plotting.

Examples

data(chromosome17)

# First genomic dependency model from screening chromosomal arm
models <- screen.cgh.mrna(geneExp, geneCopyNum, 10, chr=17, arm='p')
model <- models[[1]]

# Printing information of the model
model

# Latent variable Z
getZ(model, geneExp,geneCopyNum)

# Contributions of samples and variables to model
plot(model,geneExp,geneCopyNum)

pint documentation built on Oct. 31, 2019, 2:41 a.m.