DOI: 10.18129/B9.bioc.pbcmc    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.8 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see pbcmc.

Permutation-Based Confidence for Molecular Classification

Bioconductor version: 3.8

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

Maintainer: Cristobal Fresno <cristobalfresno at gmail.com>

Citation (from within R, enter citation("pbcmc")):


To install this package, start R (version "3.5") and enter:

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biocViews Classification, Clustering, DifferentialExpression, GeneExpression, KEGG, Microarray, MultipleComparison, Normalization, OneChannel, QualityControl, RNASeq, Software, TwoChannel, mRNAMicroarray
Version 1.10.1
In Bioconductor since BioC 3.3 (R-3.3) (3 years)
License GPL (>=2)
Depends R (>= 3.4), genefu
Imports Biobase, BiocGenerics, BiocParallel(>= 1.3.13), parallel, reshape2, grid, utils, cowplot, methods, limma, ggplot2, gridExtra, grDevices, stats
Suggests breastCancerUPP, breastCancerNKI, breastCancerVDX, breastCancerTRANSBIG, breastCancerMAINZ, breastCancerUNT
URL http://www.bdmg.com.ar/
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