pbcmc

This package is for version 3.7 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: 3.7

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 (version "3.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("pbcmc")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("pbcmc")
PermutationBased Confidence for Molecular Class PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Clustering, DifferentialExpression, GeneExpression, KEGG, Microarray, MultipleComparison, Normalization, OneChannel, QualityControl, RNASeq, Software, TwoChannel, mRNAMicroarray
Version 1.8.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements
URL http://www.bdmg.com.ar/
See More
Suggests breastCancerUPP, breastCancerNKI, breastCancerVDX, breastCancerTRANSBIG, breastCancerMAINZ, breastCancerUNT
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me MIGSA
Links To Me
Build Report Build Report

Package Archives

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

Source Package pbcmc_1.8.0.tar.gz
Windows Binary pbcmc_1.8.0.zip
Mac OS X 10.11 (El Capitan) pbcmc_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/pbcmc
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/pbcmc
Package Short Url https://bioconductor.org/packages/pbcmc/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive