pbcmc: Permutation-Based Confidence for Molecular Classification
Version 1.4.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorCristobal Fresno, German A. Gonzalez, Andrea S. Llera and Elmer A. Fernandez
Bioconductor views Classification Clustering DifferentialExpression GeneExpression KEGG Microarray MultipleComparison Normalization OneChannel QualityControl RNASeq TwoChannel mRNAMicroarray
Date of publicationNone
MaintainerCristobal Fresno <cristobalfresno@gmail.com>
LicenseGPL (>=2)
Version1.4.0
URL http://www.bdmg.com.ar/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("pbcmc")

Man pages

MolecularPermutationClassifier-class: Class 'MolecularPermutationClassifier' S4 implementation in R
MolecularPermutationClassifierConstructor: MolecularPermutationClassifier high level constructor
MolecularPermutationClassifierGenerics: Virtual functions for MolecularPermutationClassifier...
MolecularPermutationClassifierGetseters: Accessors for MolecularPermutationClassifier child class...
MolecularPermutationClassifierShow: 'Show' a MolecularPermutationClassifier subclass object
PAM50-class: PAM50 S4 implementation in R
PAM50Classify: 'classify' subjects with PAM50 molecular signature
PAM50Constructor: 'PAM50' high level coerce functions
PAM50Filtrate: 'filtrate' centroid genes from PAM50 classification
PAM50Permutate: 'permutate' subject gene-expression for PAM50 confidence
PAM50SubjectReport: PAM50 permutation test results reports
PAM50Subtype: Subject 'subtypes' for PAM50 adaptation with permuted...
pbcmcData: Example PAM50 objects for pbcmc package
pbcmcPackage: Permutation-Based Confidence for Molecular Classification...

Functions

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

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/MolecularPermutationClassifierClass.R
R/MolecularPermutationClassifierConstructor.R
R/MolecularPermutationClassifierGenerics.R
R/MolecularPermutationClassifierGetseters.R
R/MolecularPermutationClassifierShow.R
R/PAM50Class.R
R/PAM50Classify.R
R/PAM50Constructor.R
R/PAM50Filtrate.R
R/PAM50Permutate.R
R/PAM50Report.R
R/PAM50Subtype.R
R/pbcmcData.R
R/pbcmcPackage.R
build
build/vignette.rds
data
data/datalist
data/pam50centroids.RData
inst
inst/doc
inst/doc/pbcmc-vignette.R
inst/doc/pbcmc-vignette.Rnw
inst/doc/pbcmc-vignette.pdf
inst/unitTests
inst/unitTests/test_pbcmc.R
man
man/MolecularPermutationClassifier-class.Rd
man/MolecularPermutationClassifierConstructor.Rd
man/MolecularPermutationClassifierGenerics.Rd
man/MolecularPermutationClassifierGetseters.Rd
man/MolecularPermutationClassifierShow.Rd
man/PAM50-class.Rd
man/PAM50Classify.Rd
man/PAM50Constructor.Rd
man/PAM50Filtrate.Rd
man/PAM50Permutate.Rd
man/PAM50SubjectReport.Rd
man/PAM50Subtype.Rd
man/pbcmcData.Rd
man/pbcmcPackage.Rd
tests
tests/runTests.R
vignettes
vignettes/pbcmc-vignette.Rnw
vignettes/pbcmc-vignette.bib
vignettes/pbcmc.pdf
vignettes/pbcmc.xml
pbcmc documentation built on May 20, 2017, 9:46 p.m.