Last data update: 2014.03.03
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pbcmc
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 <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: 2016-05-04 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
MolecularPermutationClassifierConstructor
html
MolecularPermutationClassifierGenerics
html
MolecularPermutationClassifierGetseters
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
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