pbcmc (version 1.0.0)

loadBCDataset: 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))  
"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.

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  
}