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Last data update: 2014.03.03

R: Class "GeneDependencyModel"

GeneDependencyModel-class

R Documentation

Class "GeneDependencyModel"

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 ohuovila@gmail.com

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(pint)
Loading required package: mvtnorm
Loading required package: Matrix
Loading required package: dmt
Loading required package: MASS

dmt Copyright (C) 2008-2013 Leo Lahti and Olli-Pekka Huovilainen.
This program comes with ABSOLUTELY NO
WARRANTY.
This is free software, and you are welcome to redistribute it
under the FreeBSD license.



pint Copyright (C) 2008-2013 Olli-Pekka Huovilainen and Leo Lahti.

This program comes with ABSOLUTELY NO WARRANTY.
This is free software, and you are welcome to redistribute it
under the FreeBSD license.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/pint/GeneDependencyModel-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GeneDependencyModel-class
> ### Title: Class "GeneDependencyModel"
> ### Aliases: GeneDependencyModel-class setLoc<- setGeneName<-
> ###   setChromosome<- setArm<- getScore getLoc
> ###   setLoc<-,GeneDependencyModel-method
> ###   setGeneName<-,GeneDependencyModel-method
> ###   setChromosome<-,GeneDependencyModel-method
> ###   setArm<-,GeneDependencyModel-method
> ###   getScore,GeneDependencyModel-method getLoc,GeneDependencyModel-method
> ###   getGeneName,GeneDependencyModel-method
> ###   getWindowSize,GeneDependencyModel-method
> ###   getChromosome,GeneDependencyModel-method
> ###   getArm,GeneDependencyModel-method getZ,GeneDependencyModel-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> data(chromosome17)
> 
> # First genomic dependency model from screening chromosomal arm
> models <- screen.cgh.mrna(geneExp, geneCopyNum, 10, chr=17, arm='p')
Imputing missing values..
Imputing missing values..
Matching probes between the data sets..
Calculating dependency models for 17p with method pSimCCA, window size:10
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> model <- models[[1]]
> 
> # Printing information of the model
> model
*** matched case Wx = Wy with unconstrained W. Check covariances from parameters. dependency model for window size: 10 *** 
Gene: ENSG00000108953  Location: 17p, 1.1949Mbp
Dependency score: 0.02688904 
- WX: [1:10, 1:1]  -0.0330  0.0788 -0.0572  0.1068 ...
- WY: [1:10, 1:1]  -0.0330  0.0788 -0.0572  0.1068 ...
- phiX: [1:10, 1:10]   0.0917 -0.0121 -0.0148  0.0471 ...
- phiY: [1:10, 1:10]   0.3057  0.0313 -0.0998  0.0445 ...
************************************************
> 
> # Latent variable Z
> getZ(model, geneExp,geneCopyNum)
            S1        S2         S3        S4         S5         S6        S7
[1,] 0.4516152 -0.669576 -0.1869619 0.2215708 -0.1391644 -0.6045729 0.2544856
            S8         S9        S10       S11       S12       S13        S14
[1,] 0.2913774 -0.3416143 0.02128057 0.6240733 -1.562507 0.2730049 -0.6781598
            S15       S16        S17         S18       S19       S20        S21
[1,] 0.09662121 0.2918506 -0.2893092 -0.03086981 0.3331657 0.4022143 -0.3155861
          S22         S23        S24        S25        S26         S27
[1,] 0.057567 -0.02290406 0.06943918 0.02649978 -0.3570312 -0.06747664
           S28       S29       S30      S31       S32     S33      S34
[1,] 0.6738301 -1.016544 0.2332853 1.239983 0.2390863 1.00107 1.197374
            S35        S36       S37       S38      S39        S40         S41
[1,] -0.2065238 -0.4542886 0.5166617 0.2484803 1.448722 -0.3500769 -0.03297817
            S42        S43        S44        S45         S46       S47
[1,] -0.2194966 0.06724493 0.06934309 -0.6142182 -0.04072268 0.1662846
           S48       S49        S50      S51
[1,] -0.533165 -0.540564 0.08250099 -1.32432
> 
> # Contributions of samples and variables to model
> plot(model,geneExp,geneCopyNum)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>