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
|
This package is for version 3.3 of Bioconductor; for the stable, up-to-date release version, see pbcmc.
Permutation-Based Confidence for Molecular Classification
Bioconductor version: 3.3
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")
| R Script | PermutationBased Confidence for Molecular Class | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Classification, Clustering, DifferentialExpression, GeneExpression, KEGG, Microarray, MultipleComparison, Normalization, OneChannel, QualityControl, RNASeq, Software, TwoChannel, mRNAMicroarray |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (< 6 months) |
| 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 |
| LinkingTo | |
| Suggests | breastCancerUPP, breastCancerNKI, breastCancerVDX, breastCancerTRANSBIG, breastCancerMAINZ, breastCancerUNT |
| SystemRequirements | |
| Enhances | |
| URL | http://www.bdmg.com.ar/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | pbcmc_1.0.0.tar.gz |
| Windows Binary | pbcmc_1.0.0.zip |
| Mac OS X 10.9 (Mavericks) | pbcmc_1.0.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/pbcmc/tree/release-3.3 |
| Package Short Url | http://bioconductor.org/packages/pbcmc/ |
| Package Downloads Report | Download Stats |
Documentation »
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