Class "GenomeModels"

Description

Collection of dependency models fitting two data sets in whole genome. The dependency models are in a list of ChromosomeModelss (which represents each chromosome) that have a list of dependency models in that chromosomal arm.

Objects from the Class

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

Slots

chromosomeModels

a list of ChromosomeModels of all chromosomes

method

a string with name of the method used in dependency model

params

a list of parameters of the method

Methods

[[

signature(x = "GenomeModels"): Returns a ChromosomeModels from the list. X and Y chromosomes can be accessed with 23 and 24 or 'X' and 'Y'

[[<-

signature(x = "GenomeModels"): Attaches a ChromosomeModels to the list. X and Y chromosomes can be accessed with 23 and 24 or 'X' and 'Y'

getModelMethod

signature(model = "GenomeModels"): Returns the name of the used method

getParams

signature(model = "GenomeModels"): Returns a list of used parameters for the method

getChr

signature(model = "GenomeModels"): Returns the chromosome

getWindowSize

signature(model = "GenomeModels"): Returns the size of the window used in the dependency models.

getModelNumbers

signature(model = "GenomeModels"): Returns the total number of the dependency models.

topGenes

signature(model = "GenomeModels", 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 = "GenomeModels", num = "numeric"): Returns a list with given number of dependency models which have the highest dependency score. By default returns one model.

orderGenes

signature(model = "GenomeModels"): Returns a data frame with gene names and their model scores sorted

findModel

signature(model = "GenomeModels"): Finds a dependency model by gene name and returns it.

as.data.frame

signature(x = "GenomeModels"): converts dependency models as a dataframe with eachs row representing a dependency model for one gene. The columns are: geneName,dependencyScore,chr,arm,loc

Author(s)

Olli-Pekka Huovilainen

See Also

For calculation of dependency models for chromosomal arm: screen.cgh.mrna. This class holds a number of GeneDependencyModel in each ChromosomeModels. For plotting dependency scores see dependency score plotting.