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pint (version 1.22.0)

ChromosomeModels-class: Class "ChromosomeModels"

Description

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

Arguments

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
.

See Also

For calculation of dependency models for chromosomal arm: screen.cgh.mrna. This class holds a number of GeneDependencyModel objects. For plotting dependency scores see dependency score plotting. Dependency models for whole genome: GenomeModels.

Examples

Run this code
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)

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