Permutation-Based Confidence for Molecular Classification


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Documentation for package ‘pbcmc’ version 1.0.0

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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