ChromosomeModels-class: Class "ChromosomeModels"

In pint: Pairwise INTegration of functional genomics data

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 [e-mail]

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)

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