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Last data update: 2014.03.03

R: Class "ChromosomeModels"

ChromosomeModels-class

R Documentation

Class "ChromosomeModels"

Description

Collection of dependency models fitting two data sets in particular chromosome.

Objects from the Class

Function screen.cgh.mrna and screen.cgh.mir returns an object of this class.

Slots

models: a list of GeneDependencyModels
chromosome: the number of chromosome
method: a string with name of the method used in dependency models
params: a list of parameters of the used method

Methods

[[: signature(x = "ChromosomeModels"): Returns the model from the list or returns the dependency models of the arm specified with 'p' or 'q'
[[<-: signature(x = "ChromosomeModels"): Attaches the a model to the list
getChromosome: signature(model = "ChromosomeModels"): Returns the chromosome
getArm: signature(model = "ChromosomeModels"): Returns a vector of arms where corresponding dependency model has been calculated.
getLoc: signature(model = "ChromosomeModels"): Returns a vector of locations of the genomic dependency models.
getScore: signature(model = "ChromosomeModels"): Returns a vector of the scores of the genomic dependency models.
getPArm: signature(model = "ChromosomeModels"): Returns the dependency models of the p arm which is of class ChromosomeModels
getQArm: signature(model = "ChromosomeModels"): Returns the dependency models of the q arm which is of class ChromosomeModels
getModelMethod: signature(model = "ChromosomeModels"): Returns the name of the used method
getParams: signature(model = "ChromosomeModels"): Returns a list of used parameters for the method
getWindowSize: signature(model = "ChromosomeModels"): Returns the size of the window used in the dependency models.
topGenes: signature(model = "ChromosomeModels", num = "numeric"): Returns a vector of given number of names of the genes which have the highest dependency score. With default value num = NA returns all the genes.
topModels: signature(model = "ChromosomeModels", num = "numeric"): Returns a list with given number of dependency models which have the highest dependency score. By default returns one model.
isEmpty: signature(model = "ChromosomeModels"): Returns TRUE if model has no dependency models
orderGenes: signature(model = "ChromosomeModels"): Returns a data frame with gene names and their model scores sorted
findModel: signature(model = "ChromosomeModels"): Finds a dependency model by gene name and returns it.
as.data.frame: signature(x = "ChromosomeModels"): converts dependency models as a dataframe with eachs row representing a dependency models for one gene. The columns are: geneName,dependencyScore,chr,arm,loc. If arm information has not been given to screening function, arm column is omitted

Author(s)

Olli-Pekka Huovilainen ohuovila@gmail.com

Examples

data(chromosome17)

## calculate dependency models over chromosome 17
model17 <- screen.cgh.mrna(geneExp, geneCopyNum, windowSize = 10, chr
= 17)

model17

## Information of the dependency model which has the highest dependency score
topGenes(model17, 1)

## Finding a dependency model by its name
findModel(model17, "ENSG00000129250")

## Information of the first dependency model
model17[[1]]

#Plotting
plot(model17)

# genes in p arm with the highest dependency scores
topGenes(model17[['p']], 5)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
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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/ChromosomeModels-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ChromosomeModels-class
> ### Title: Class "ChromosomeModels"
> ### Aliases: ChromosomeModels-class getPArm getQArm [[ [[<- getChromosome
> ###   getArm getGeneName getModelMethod getParams getWindowSize topGenes
> ###   topModels getModelNumbers isEmpty orderGenes findModel
> ###   [[,ChromosomeModels-method [[<-,ChromosomeModels-method
> ###   getChromosome,ChromosomeModels-method getPArm,ChromosomeModels-method
> ###   getQArm,ChromosomeModels-method getArm,ChromosomeModels-method
> ###   getGeneName,ChromosomeModels-method getLoc,ChromosomeModels-method
> ###   getScore,ChromosomeModels-method
> ###   getModelMethod,ChromosomeModels-method
> ###   getParams,ChromosomeModels-method
> ###   getWindowSize,ChromosomeModels-method
> ###   topGenes,ChromosomeModels-method topModels,ChromosomeModels-method
> ###   getModelNumbers,ChromosomeModels-method
> ###   isEmpty,ChromosomeModels-method orderGenes,ChromosomeModels-method
> ###   findModel,ChromosomeModels-method isEmpty,ChromosomeModels-method
> ###   [[,ChromosomeModels-method as.data.frame,ChromosomeModels-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> data(chromosome17)
> 
> ## calculate dependency models over chromosome 17
> model17 <- screen.cgh.mrna(geneExp, geneCopyNum, windowSize = 10, chr
+ = 17)
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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Calculating dependency models for 17q with method pSimCCA, window size:10
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> 
> model17
*** Dependency models for chromosome: 17 ***
Method used: pSimCCA with window size 10 
Number of models in 17p: 366, 17q: 366
Summary of dependency scores: 
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
0.009852 0.021880 0.028740 0.039430 0.037140 0.263600 
******************************************
> 
> ## Information of the dependency model which has the highest dependency score
> topGenes(model17, 1)
[1] "ENSG00000141738"
> 
> ## Finding a dependency model by its name
> findModel(model17, "ENSG00000129250")
*** matched case Wx = Wy with unconstrained W. Check covariances from parameters. dependency model for window size: 10 *** 
Gene: ENSG00000129250  Location: 17p, 4.8686Mbp
Dependency score: 0.02380812 
- WX: [1:10, 1:1]   0.0389 -0.0559  0.0238 -0.0679 ...
- WY: [1:10, 1:1]   0.0389 -0.0559  0.0238 -0.0679 ...
- phiX: [1:10, 1:10]   0.04592  0.01705 -0.01154  0.00432 ...
- phiY: [1:10, 1:10]   0.1835  0.0244  0.0222 -0.0842 ...
************************************************
> 
> ## Information of the first dependency model
> model17[[1]]
*** 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 ...
************************************************
> 
> #Plotting
> plot(model17)
> 
> # genes in p arm with the highest dependency scores
> topGenes(model17[['p']], 5)
[1] "ENSG00000179094,ENSG00000179036" "ENSG00000179036"                
[3] "ENSG00000178921"                 "ENSG00000170175"                
[5] "ENSG00000133028"                
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>