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

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

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)