biosigner: Signature discovery from omics data

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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.

Author
Philippe Rinaudo <phd.rinaudo@gmail.com>, Etienne Thevenot <etienne.thevenot@cea.fr>
Date of publication
None
Maintainer
Philippe Rinaudo <phd.rinaudo@gmail.com>, Etienne Thevenot <etienne.thevenot@cea.fr>
License
CeCILL
Version
1.2.4

View on Bioconductor

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

Files in this package

biosigner/DESCRIPTION
biosigner/NAMESPACE
biosigner/NEWS
biosigner/R
biosigner/R/allClasses.R
biosigner/R/allGenerics.R
biosigner/R/biosigner-package.R
biosigner/R/datasets.R
biosigner/R/helpers.R
biosigner/R/methods.R
biosigner/build
biosigner/build/vignette.rds
biosigner/data
biosigner/data/datalist
biosigner/data/diaplasma.rdata
biosigner/inst
biosigner/inst/CITATION
biosigner/inst/doc
biosigner/inst/doc/biosigner-vignette.R
biosigner/inst/doc/biosigner-vignette.Rmd
biosigner/inst/doc/biosigner-vignette.pdf
biosigner/inst/unitTests
biosigner/inst/unitTests/test_biosigner.R
biosigner/man
biosigner/man/biosign-class.Rd
biosigner/man/biosign.Rd
biosigner/man/biosigner-package.Rd
biosigner/man/diaplasma.Rd
biosigner/man/getAccuracyMN.Rd
biosigner/man/getSignatureLs.Rd
biosigner/man/plot.Rd
biosigner/man/predict.Rd
biosigner/man/show.Rd
biosigner/tests
biosigner/tests/runTests.R
biosigner/vignettes
biosigner/vignettes/biosigner-vignette.Rmd
biosigner/vignettes/biosigner-vignette.bib