Last data update: 2014.03.03


Package: pbcmc
Type: Package
Title: Permutation-Based Confidence for Molecular Classification
Version: 1.0.0
Date: 2016-04-04
Author: Cristobal Fresno, German A. Gonzalez, Andrea S. Llera and Elmer
A. Fernandez
Maintainer: Cristobal Fresno <>
Description: 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.
License: GPL (>=2)
Depends: R (>= 3.3.0), 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
biocViews: Classification, GeneExpression, Microarray,
MultipleComparison, QualityControl, Normalization, Clustering,
mRNAMicroarray, OneChannel, TwoChannel, RNASeq, KEGG,
Collate: 'pbcmcPackage.R' 'MolecularPermutationClassifierClass.R'
'MolecularPermutationClassifierShow.R' 'PAM50Class.R'
'PAM50Classify.R' 'PAM50Constructor.R' 'PAM50Filtrate.R'
'PAM50Permutate.R' 'PAM50Report.R' 'PAM50Subtype.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-04 06:57:17 UTC; biocbuild

● BiocViews: Classification, Clustering, DifferentialExpression, GeneExpression, KEGG, Microarray, MultipleComparison, Normalization, OneChannel, QualityControl, RNASeq, TwoChannel, mRNAMicroarray
3 images, 13 functions, 1 datasets
● Reverse Depends: 0

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'pbcmc' ...
** R
** data
** inst
** preparing package for lazy loading
No methods found in "BiocGenerics" for requests: unlist
Creating a generic function for 'summary' from package 'base' in package 'pbcmc'
** help
*** installing help indices
  converting help for package 'pbcmc'
    finding HTML links ... done
    MolecularPermutationClassifier-class    html  
    MolecularPermutationClassifierShow      html  
    PAM50-class                             html  
    PAM50Classify                           html  
    PAM50Constructor                        html  
    finding level-2 HTML links ... done

    PAM50Filtrate                           html  
    PAM50Permutate                          html  
    PAM50SubjectReport                      html  
    PAM50Subtype                            html  
    pbcmcData                               html  
    pbcmcPackage                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "BiocGenerics" for requests: unlist
* DONE (pbcmc)
Making 'packages.html' ... done