pbcmc: Permutation-Based Confidence for Molecular Classification

The pbcmc package characterizes uncertainty assessment on gene expression classifiers, a. k. a. molecular signatures, based on a permutation test. In order to achieve this goal, synthetic simulated subjects are obtained by permutations of gene labels. Then, each synthetic subject is tested against the corresponding subtype classifier to build the null distribution. Thus, classification confidence measurement can be provided for each subject, to assist physician therapy choice. At present, it is only available for PAM50 implementation in genefu package but it can easily be extend to other molecular signatures.

AuthorCristobal Fresno, German A. Gonzalez, Andrea S. Llera and Elmer A. Fernandez
Date of publicationNone
MaintainerCristobal Fresno <cristobalfresno@gmail.com>
LicenseGPL (>=2)

View on Bioconductor


annotation Man page
annotation<- Man page
annotation<-,MolecularPermutationClassifier,ANY-method Man page
annotation,MolecularPermutationClassifier-method Man page
as Man page
as.PAM50 Man page
as.PAM50,MAList-method Man page
as.PAM50-methods Man page
classification Man page
classification-methods Man page
classification,MolecularPermutationClassifier-method Man page
classify Man page
classify-methods Man page
classify,PAM50-method Man page
databaseReport Man page
databaseReport-methods Man page
databaseReport,PAM50-method Man page
exprs Man page
exprs<- Man page
exprs<-,MolecularPermutationClassifier,ANY-method Man page
exprs,MolecularPermutationClassifier-method Man page
filtrate Man page
filtrate-methods Man page
filtrate,PAM50-method Man page
loadBCDataset Man page
loadBCDataset,classGeneratorFunction-method Man page
loadBCDataset-methods Man page
MolecularPermutationClassifier-class Man page
PAM50 Man page
pam50centroids Man page
PAM50-class Man page
parameters Man page
parameters<- Man page
parameters<--methods Man page
parameters-methods Man page
parameters<-,MolecularPermutationClassifier-method Man page
parameters,MolecularPermutationClassifier-method Man page
pbcmcPackage Man page
pbcmcPackage-package Man page
permutate Man page
permutate-methods Man page
permutate,PAM50-method Man page
permutation Man page
permutation-methods Man page
permutation,MolecularPermutationClassifier-method Man page
show Man page
show,MolecularPermutationClassifier-method Man page
subjectReport Man page
subjectReport-methods Man page
subjectReport,PAM50-method Man page
subtypes Man page
subtypes-methods Man page
subtypes,PAM50-method Man page
summary,PAM50-method Man page
targets Man page
targets<- Man page
targets<--methods Man page
targets-methods Man page
targets<-,MolecularPermutationClassifier-method Man page
targets,MolecularPermutationClassifier-method Man page

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