GenomeModels-class: 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. 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
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.