biosigner: Signature discovery from omics data
Version 1.4.0

Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a new method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets. A Galaxy implementation of the package is available within the Workflow4metabolomics.org online infrastructure for computational metabolomics.

Browse man pages Browse package API and functions Browse package files

AuthorPhilippe Rinaudo <phd.rinaudo@gmail.com>, Etienne Thevenot <etienne.thevenot@cea.fr>
Bioconductor views Classification FeatureExtraction Lipidomics Metabolomics Proteomics Transcriptomics
Date of publicationNone
MaintainerPhilippe Rinaudo <phd.rinaudo@gmail.com>, Etienne Thevenot <etienne.thevenot@cea.fr>
LicenseCeCILL
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("biosigner")

Man pages

biosign: Builds the molecular signature.
biosign-class: Class "biosign"
biosigner-package: Molecular signature discovery from omics data
diaplasma: Analysis of plasma from diabetic patients by LC-HRMS
getAccuracyMN: Accuracies of the full model and the models restricted to the...
getSignatureLs: Signatures selected by the models
plot: Plot method for 'biosign' signature objects
predict: Predict method for 'biosign' signature objects
show: Show method for 'biosign' signature objects

Functions

biosign Man page
biosign,ExpressionSet-method Man page
biosign,data.frame-method Man page
biosign,matrix-method Man page
biosign-class Man page
biosigner Man page
biosigner-package Man page
bootExtractF Source code
diaplasma Man page
getAccuracyF Source code
getAccuracyMN Man page
getAccuracyMN,biosign-method Man page
getBootModelF Source code
getBootSignificanceF Source code
getBootSummaryF Source code
getBootTestIndF Source code
getBootTestxF Source code
getBootTestyF Source code
getBootTrainxF Source code
getBootTrainyF Source code
getImportanceF Source code
getModelAccuRankF Source code
getModelF Source code
getPredictionF Source code
getSignatureLs Man page
getSignatureLs,biosign-method Man page
getSignificanceF Source code
getTierF Source code
plot,biosign-method Man page
plot.biosign Man page
predict,biosign-method Man page
predict.biosign Man page
show,biosign-method Man page
show.biosign Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/allClasses.R
R/allGenerics.R
R/biosigner-package.R
R/datasets.R
R/helpers.R
R/methods.R
build
build/vignette.rds
data
data/datalist
data/diaplasma.rdata
inst
inst/CITATION
inst/doc
inst/doc/biosigner-vignette.R
inst/doc/biosigner-vignette.Rmd
inst/doc/biosigner-vignette.pdf
inst/unitTests
inst/unitTests/test_biosigner.R
man
man/biosign-class.Rd
man/biosign.Rd
man/biosigner-package.Rd
man/diaplasma.Rd
man/getAccuracyMN.Rd
man/getSignatureLs.Rd
man/plot.Rd
man/predict.Rd
man/show.Rd
tests
tests/runTests.R
vignettes
vignettes/biosigner-vignette.Rmd
vignettes/biosigner-vignette.bib
biosigner documentation built on May 20, 2017, 10:59 p.m.