# Permutation-Based Confidence for Molecular Classification

## Documentation for package ‘pbcmc’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

pbcmcPackage-package | Permutation-Based Confidence for Molecular Classification (pbcmc)
annotation | Accessors for MolecularPermutationClassifier child class slots
annotation-method | Accessors for MolecularPermutationClassifier child class slots
annotation<- | Accessors for MolecularPermutationClassifier child class slots
annotation<--method | Accessors for MolecularPermutationClassifier child class slots
as | 'PAM50' high level coerce functions
as.PAM50 | 'PAM50' high level coerce functions
as.PAM50-method | 'PAM50' high level coerce functions
as.PAM50-methods | 'PAM50' high level coerce functions
classification | Accessors for MolecularPermutationClassifier child class slots
classification-method | Accessors for MolecularPermutationClassifier child class slots
classification-methods | Accessors for MolecularPermutationClassifier child class slots
classify | Virtual functions for MolecularPermutationClassifier hierarchy
classify-method | 'classify' subjects with PAM50 molecular signature
classify-methods | Virtual functions for MolecularPermutationClassifier hierarchy
databaseReport | Virtual functions for MolecularPermutationClassifier hierarchy
databaseReport-method | PAM50 permutation test results reports
databaseReport-methods | Virtual functions for MolecularPermutationClassifier hierarchy
exprs | Accessors for MolecularPermutationClassifier child class slots
exprs-method | Accessors for MolecularPermutationClassifier child class slots
exprs<- | Accessors for MolecularPermutationClassifier child class slots
exprs<--method | Accessors for MolecularPermutationClassifier child class slots
filtrate | Virtual functions for MolecularPermutationClassifier hierarchy
filtrate-method | 'filtrate' centroid genes from PAM50 classification
filtrate-methods | Virtual functions for MolecularPermutationClassifier hierarchy
loadBCDataset | MolecularPermutationClassifier high level constructor
loadBCDataset-method | MolecularPermutationClassifier high level constructor
loadBCDataset-methods | MolecularPermutationClassifier high level constructor
MolecularPermutationClassifier-class | Class 'MolecularPermutationClassifier' S4 implementation in R
PAM50 | PAM50 S4 implementation in R
PAM50-class | PAM50 S4 implementation in R
pam50centroids | Example PAM50 objects for pbcmc package
parameters | Accessors for MolecularPermutationClassifier child class slots
parameters-method | Accessors for MolecularPermutationClassifier child class slots
parameters-methods | Accessors for MolecularPermutationClassifier child class slots
parameters<- | Accessors for MolecularPermutationClassifier child class slots
parameters<--method | Accessors for MolecularPermutationClassifier child class slots
parameters<--methods | Accessors for MolecularPermutationClassifier child class slots
pbcmcPackage | Permutation-Based Confidence for Molecular Classification (pbcmc)
permutate | Virtual functions for MolecularPermutationClassifier hierarchy
permutate-method | 'permutate' subject gene-expression for PAM50 confidence
permutate-methods | Virtual functions for MolecularPermutationClassifier hierarchy
permutation | Accessors for MolecularPermutationClassifier child class slots
permutation-method | Accessors for MolecularPermutationClassifier child class slots
permutation-methods | Accessors for MolecularPermutationClassifier child class slots
show | 'Show' a MolecularPermutationClassifier subclass object
show-method | 'Show' a MolecularPermutationClassifier subclass object
subjectReport | Virtual functions for MolecularPermutationClassifier hierarchy
subjectReport-method | PAM50 permutation test results reports
subjectReport-methods | Virtual functions for MolecularPermutationClassifier hierarchy
subtypes | Virtual functions for MolecularPermutationClassifier hierarchy
subtypes-method | Subject 'subtypes' for PAM50 adaptation with permuted results.
subtypes-methods | Virtual functions for MolecularPermutationClassifier hierarchy
summary-method | PAM50 permutation test results reports
targets | Accessors for MolecularPermutationClassifier child class slots
targets-method | Accessors for MolecularPermutationClassifier child class slots
targets-methods | Accessors for MolecularPermutationClassifier child class slots
targets<- | Accessors for MolecularPermutationClassifier child class slots
targets<--method | Accessors for MolecularPermutationClassifier child class slots
targets<--methods | Accessors for MolecularPermutationClassifier child class slots