MolecularPermutationClassifier-class: Class 'MolecularPermutationClassifier' S4 implementation in R

Description Slots Superclasses Subclasses Functions Author(s) References See Also


Virtual class to represent gene-based molecular signature classification by means of permutation test.



named list with at least the following fields:


integer with number of permutations. Default: 1e4L


character with significant value used. Default value is "fdr".


numeric with p-value or fdr cutoff used, i.e., variable<pCutoff. Default: 0.01


should null distribution simulation values be kept?. Default: FALSE


matrix with gene exprs profile, where genes are in rows and subjects as columns, a.k.a., M matrix.


data.frame with individual annotations (genes, etc). Minimal compulsory fields are:


same characters as in row.names(M).


integer with NCBI Entrez Data Base.


character with gene mnemonic, a.k.a. gene symbol.


data.frame with additional subject data (optional).


named list with at least the following fields:


factor with all possible class levels.


named list with at least the following fields:


numeric matrix with subjects in row and classes in columns.


numeric matrix with False Discovery Rate correction of p-values by row.


None declared.



Peruo et al. (2000 and 2010) breast cancer subtypes, i. e., Luminal A, Luminal B, Basal, Her2 or Normal-like subtypes as implemented in genefu library (Haibe-Kains et al. 2014).


MolecularPermutationClassifier S4 class includes the following functions:


Cristobal Fresno, German A. Gonzalez, Andrea S. Llera and Elmer Andres Fernandez


  1. Haibe-Kains B, Schroeder M, Bontempi G, Sotiriou C and Quackenbush J, 2014, genefu: Relevant Functions for Gene Expression Analysis, Especially in Breast Cancer. R package version 1.16.0,

  2. Perou CM, Sorlie T, Eisen MB, et al., 2000, Molecular portraits of human breast tumors. Nature 406:747-752

  3. Perou CM, Parker JS, Prat A, Ellis MJ, Bernard PB., 2010, Clinical implementation of the intrinsic subtypes of breast cancer, The Lancet Oncology 11(8):718-719

See Also

PAM50 for a complete example, loadBCDataset to load BreastCancerXX dataset, filtrate, classify and permutate to get corresponding Breast Cancer subtype. Getters/Setters for this class are parameters, exprs, annotation, targets, classification and permutation.

Other MolecularPermutationClassifier: parameters, show

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