ChromosomeModels-class {pint} | R Documentation |
Collection of dependency models fitting two data sets in particular chromosome.
Function
screen.cgh.mrna
and screen.cgh.mir
returns an object of this class.
a list of GeneDependencyModels
the number of chromosome
a string with name of the method used in dependency models
a list of parameters of the used method
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
signature(model = "ChromosomeModels")
:
Returns the chromosome
signature(model = "ChromosomeModels")
:
Returns a vector of arms where corresponding dependency model has been calculated.
signature(model = "ChromosomeModels")
:
Returns a vector of locations of the genomic dependency models.
signature(model = "ChromosomeModels")
:
Returns a vector of the scores of the genomic dependency models.
signature(model = "ChromosomeModels")
: Returns
the dependency models of the p arm which is of class
ChromosomeModels
signature(model = "ChromosomeModels")
: Returns
the dependency models of the q arm which is of class
ChromosomeModels
signature(model = "ChromosomeModels")
:
Returns the name of the used method
signature(model = "ChromosomeModels")
:
Returns a list of used parameters for the method
signature(model = "ChromosomeModels")
:
Returns the size of the window used in the dependency models.
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.
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.
signature(model = "ChromosomeModels")
: Returns
TRUE if model
has no dependency models
signature(model = "ChromosomeModels")
:
Returns a data frame with gene names and their model scores sorted
signature(model = "ChromosomeModels")
:
Finds a dependency model by gene name and returns it.
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
.
Olli-Pekka Huovilainen ohuovila@gmail.com
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.
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)