GenomeModels-class: Class "GenomeModels"
In pint: Pairwise INTegration of functional genomics data

Description Objects from the Class Slots Methods Author(s) See Also

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.

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

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

[[: 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

Olli-Pekka Huovilainen

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.

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