To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("pbcmc")

In most cases, you don't need to download the package archive at all.

pbcmc

 

   

Permutation-Based Confidence for Molecular Classification

Bioconductor version: Release (3.5)

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")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("pbcmc")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("pbcmc")

 

PDF R Script PermutationBased Confidence for Molecular Class
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, Clustering, DifferentialExpression, GeneExpression, KEGG, Microarray, MultipleComparison, Normalization, OneChannel, QualityControl, RNASeq, Software, TwoChannel, mRNAMicroarray
Version 1.4.0
In Bioconductor since BioC 3.3 (R-3.3) (1 year)
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
LinkingTo
Suggests breastCancerUPP, breastCancerNKI, breastCancerVDX, breastCancerTRANSBIG, breastCancerMAINZ, breastCancerUNT
SystemRequirements
Enhances
URL http://www.bdmg.com.ar/
Depends On Me
Imports Me
Suggests Me MIGSA
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source pbcmc_1.4.0.tar.gz
Windows Binary pbcmc_1.4.0.zip
Mac OS X 10.11 (El Capitan) pbcmc_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/pbcmc/tree/release-3.5
Package Short Url http://bioconductor.org/packages/pbcmc/
Package Downloads Report Download Stats

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