pbcmc: Permutation-Based Confidence for Molecular Classification

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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.

Author
Cristobal Fresno, German A. Gonzalez, Andrea S. Llera and Elmer A. Fernandez
Date of publication
None
Maintainer
Cristobal Fresno <cristobalfresno@gmail.com>
License
GPL (>=2)
Version
1.2.2
URLs

View on Bioconductor

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...

Files in this package

pbcmc/DESCRIPTION
pbcmc/NAMESPACE
pbcmc/NEWS
pbcmc/R
pbcmc/R/MolecularPermutationClassifierClass.R
pbcmc/R/MolecularPermutationClassifierConstructor.R
pbcmc/R/MolecularPermutationClassifierGenerics.R
pbcmc/R/MolecularPermutationClassifierGetseters.R
pbcmc/R/MolecularPermutationClassifierShow.R
pbcmc/R/PAM50Class.R
pbcmc/R/PAM50Classify.R
pbcmc/R/PAM50Constructor.R
pbcmc/R/PAM50Filtrate.R
pbcmc/R/PAM50Permutate.R
pbcmc/R/PAM50Report.R
pbcmc/R/PAM50Subtype.R
pbcmc/R/pbcmcData.R
pbcmc/R/pbcmcPackage.R
pbcmc/build
pbcmc/build/vignette.rds
pbcmc/data
pbcmc/data/datalist
pbcmc/data/pam50centroids.RData
pbcmc/inst
pbcmc/inst/doc
pbcmc/inst/doc/pbcmc-vignette.R
pbcmc/inst/doc/pbcmc-vignette.Rnw
pbcmc/inst/doc/pbcmc-vignette.pdf
pbcmc/inst/unitTests
pbcmc/inst/unitTests/test_pbcmc.R
pbcmc/man
pbcmc/man/MolecularPermutationClassifier-class.Rd
pbcmc/man/MolecularPermutationClassifierConstructor.Rd
pbcmc/man/MolecularPermutationClassifierGenerics.Rd
pbcmc/man/MolecularPermutationClassifierGetseters.Rd
pbcmc/man/MolecularPermutationClassifierShow.Rd
pbcmc/man/PAM50-class.Rd
pbcmc/man/PAM50Classify.Rd
pbcmc/man/PAM50Constructor.Rd
pbcmc/man/PAM50Filtrate.Rd
pbcmc/man/PAM50Permutate.Rd
pbcmc/man/PAM50SubjectReport.Rd
pbcmc/man/PAM50Subtype.Rd
pbcmc/man/pbcmcData.Rd
pbcmc/man/pbcmcPackage.Rd
pbcmc/tests
pbcmc/tests/runTests.R
pbcmc/vignettes
pbcmc/vignettes/pbcmc-vignette.Rnw
pbcmc/vignettes/pbcmc-vignette.bib
pbcmc/vignettes/pbcmc.pdf
pbcmc/vignettes/pbcmc.xml