MolecularPermutationClassifierConstructor: MolecularPermutationClassifier high level constructor

Description Usage Arguments Value Author(s) References See Also Examples

Description

High level constructor for MolecularPermutationClassifier subclasses using available Bioconductor's Breast Cancer example datasets.

Usage

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loadBCDataset(Class, libname = c("upp", "nki", "vdx", "mainz", "transbig", 
    "unt"), verbose = getOption("verbose", default = FALSE))  

## S4 method for signature 'classGeneratorFunction'
loadBCDataset(Class, libname = c("upp", 
    "nki", "vdx", "mainz", "transbig", "unt"), verbose = getOption("verbose", 
    default = FALSE))  

Arguments

Class

name of MolecularPermutationClassifier child class to use.

libname

lowercase character with the name of the breastCancerXXX database to be loaded. At present, XXX can be "upp", "nki", "vdx", "mainz", "transbig" or "unt". See reference for available breast cancer citations.

verbose

should the user feedback be displayed? By default value is "verbose" global option parameter, if present, or FALSE otherwise.

Value

MolecularPermutationClassifier subclass object with exprs, annotation and targets slots taken from the libname used.

Author(s)

Cristobal Fresno cfresno@bdmg.com.ar, German A. Gonzalez ggonzalez@bdmg.com.ar, Andrea S. Llera allera@leloir.org.ar and Elmer Andres Fernandez efernandez@bdmg.com.ar

References

See Also

PAM50 for a complete example.

Other MolecularPermutationClassifier PAM50: PAM50-class, filtrate

Examples

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##Using Breast Cancer NKI database, if available, to create a PAM50 class. 
if(requireNamespace("breastCancerNKI")){
    object<-loadBCDataset(Class=PAM50, libname="nki", verbose=TRUE)  
    object

    ##Now we can inspect the object   
    head(exprs(object))      ##The gene expression
    head(annotation(object)) ##The available annotation 
    head(targets(object))    ##The clinical data present in the package  
}

pbcmc documentation built on Nov. 1, 2018, 2:09 a.m.