loadBCDataset {pbcmc} | R Documentation

## MolecularPermutationClassifier high level constructor

### Description

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

### Usage

    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

- Schroeder M, Haibe-Kains B, Culhane A, Sotiriou C, Bontempi G and Quackenbush J (2011). breastCancerUPP: Gene expression dataset published by Miller et al. [2005] (UPP).. R package version 1.3.1, http://compbio.dfci.harvard.edu/.

- Schroeder M, Haibe-Kains B, Culhane A, Sotiriou C, Bontempi G and Quackenbush J (2011). breastCancerNKI: Genexpression dataset published by van't Veer et al. [2002] and van de Vijver et al. [2002] (NKI).. R package version 1.3.1, http://compbio.dfci.harvard.edu/.

- Schroeder M, Haibe-Kains B, Culhane A, Sotiriou C, Bontempi G and Quackenbush J (2011). breastCancerVDX: Gene expression datasets published by Wang et al. [2005] and Minn et al. [2007] (VDX). R package version 1.3.1, http://compbio.dfci.harvard.edu/.

- Schroeder M, Haibe-Kains B, Culhane A, Sotiriou C, Bontempi G and Quackenbush J (2011). breastCancerTRANSBIG: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG).. R package version 1.3.1, http://compbio.dfci.harvard.edu/.

- Schroeder M, Haibe-Kains B, Culhane A, Sotiriou C, Bontempi G and Quackenbush J (2011). breastCancerMAINZ: Gene expression dataset published by Schmidt et al. [2008] (MAINZ).. R package version 1.3.1, http://compbio.dfci.harvard.edu/.

- Schroeder M, Haibe-Kains B, Culhane A, Sotiriou C, Bontempi G and Quackenbush J (2011). breastCancerUNT: Gene expression dataset published by Sotiriou et al. [2007] (UNT).. R package version 1.3.1, http://compbio.dfci.harvard.edu/.

### See Also

`PAM50` for a complete example.

Other MolecularPermutationClassifier PAM50: `PAM50-class`, `filtrate`

### Examples

    ##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
    }

[Package pbcmc version 1.8.0 Index]