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("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 | R Script | |
| Reference Manual | ||
| 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 [email protected]:packages/pbcmc |
| Package Short Url | https://bioconductor.org/packages/pbcmc/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.7 | Source Archive |