pbcmc

DOI: 10.18129/B9.bioc.pbcmc    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

Permutation-Based Confidence for Molecular Classification

Bioconductor version: Release (3.8)

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 (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("pbcmc", version = "3.8")

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

Documentation

PDF   Reference Manual

Details

biocViews Classification, Clustering, DifferentialExpression, GeneExpression, KEGG, Microarray, MultipleComparison, Normalization, OneChannel, QualityControl, RNASeq, Software, TwoChannel, mRNAMicroarray
Version 1.10.1
In Bioconductor since BioC 3.3 (R-3.3) (2.5 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
LinkingTo
Suggests breastCancerUPP, breastCancerNKI, breastCancerVDX, breastCancerTRANSBIG, breastCancerMAINZ, breastCancerUNT
SystemRequirements
Enhances
URL http://www.bdmg.com.ar/
Depends On Me
Imports Me
Suggests Me MIGSA
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
Mac OS X 10.11 (El Capitan)
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 http://bioconductor.org/packages/pbcmc/
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