Package: pbcmc
Type: Package
Title: Permutation-Based Confidence for Molecular Classification
Version: 1.2.2
Date: 2016-09-23
Author: Cristobal Fresno, German A. Gonzalez, Andrea S. Llera and Elmer  
        A. Fernandez   
Maintainer: Cristobal Fresno <cristobalfresno@gmail.com>
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.  
URL: http://www.bdmg.com.ar/
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,
        DifferentialExpression
Collate: 'pbcmcPackage.R' 'MolecularPermutationClassifierClass.R'
        'MolecularPermutationClassifierConstructor.R'
        'MolecularPermutationClassifierGenerics.R'
        'MolecularPermutationClassifierGetseters.R'
        'MolecularPermutationClassifierShow.R' 'PAM50Class.R'
        'PAM50Classify.R' 'PAM50Constructor.R' 'PAM50Filtrate.R'
        'PAM50Permutate.R' 'PAM50Report.R' 'PAM50Subtype.R'
        'pbcmcData.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-12-01 01:26:02 UTC; biocbuild
Built: R 3.3.2; ; 2016-12-01 04:58:13 UTC; windows
