messina: Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems.
Version 1.12.0

Messina is a collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression.

AuthorMark Pinese [aut], Mark Pinese [cre], Mark Pinese [cph]
Bioconductor views BiomedicalInformatics Classification DifferentialExpression GeneExpression Survival
Date of publicationNone
MaintainerMark Pinese <m.pinese@garvan.org.au>
LicenseEPL (>= 1.0)
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("messina")

Getting started

Package overview

Popular man pages

messina: Find optimal single feature classifiers
messinaDE: Detect differential expression in the presence of outliers
messina-package: The Messina package for classification and outlier...
messinaSurv: Find optimal prognostic features using the Messina algorithm
messinaTopResults: Display a summary of the top results from a Messina analysis
plot-MessinaClassResult-missing-method: Plot the results of a Messina analysis on a classification /...
tcga_kirc_example: Example TCGA KIRC RNAseq expression and survival data
See all...

All man pages Function index File listing

Man pages

messina: Find optimal single feature classifiers
messinaDE: Detect differential expression in the presence of outliers
MessinaFits-class: The MessinaFits class
messina-package: The Messina package for classification and outlier...
MessinaParameters-class: The MessinaParameters class
MessinaResult-class: The MessinaResult class
messinaSurv: Find optimal prognostic features using the Messina algorithm
messinaTopResults: Display a summary of the top results from a Messina analysis
plot-MessinaClassResult-missing-method: Plot the results of a Messina analysis on a classification /...
plot-MessinaSurvResult-missing-method: Plot the results of a Messina analysis on a survival problem.
show-methods: Generic show methods for Messina objects.
tcga_kirc_example: Example TCGA KIRC RNAseq expression and survival data

Functions

MessinaClassResult-class Man page
MessinaFits-class Man page
MessinaParameters-class Man page
MessinaResult-class Man page
MessinaSurvResult-class Man page
calcBootstrapKaplanMeierEstimates Source code
calcBootstrapKaplanMeierEstimatesAtTimes Source code
calcKaplanMeierEstimates Source code
calcKaplanMeierEstimatesOnBootstrapSample Source code
kirc.exprs Man page
kirc.surv Man page
messina Man page Source code
messina-package Man page
messinaC Source code
messinaClassPlot Source code
messinaDE Man page Source code
messinaSurv Man page Source code
messinaSurvDoesObjectivePass Source code
messinaSurvFindBestThreshold Source code
messinaSurvKMplot Source code
messinaSurvKMplotSingleGroup Source code
messinaSurvObjPlot Source code
messinaSurvObjectiveFunc Source code
messinaSurvPlot Source code
messinaSurvSingleX Source code
messinaSurvSingleXDraw Source code
messinaSurvTrain Source code
messinaSurvTrainOnSubset Source code
messinaTopResults Man page Source code
plot,MessinaClassResult,missing-method Man page
plot,MessinaClassResult-method Man page
plot,MessinaSurvResult,missing-method Man page
plot,MessinaSurvResult-method Man page
show,MessinaFits-method Man page
show,MessinaParameters-method Man page
show,MessinaResult-method Man page
tcga_kirc_example Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/RcppExports.R
R/messina-package.R
R/messina.R
R/messinaSurv.R
R/messinaTopResults.R
R/plot-methods.R
R/show-methods.R
R/tcga_kirc_example-data.R
REFERENCES.bib
build
build/vignette.rds
data
data/tcga_kirc_example.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/messina.R
inst/doc/messina.Rnw
inst/doc/messina.pdf
man
man/MessinaFits-class.Rd
man/MessinaParameters-class.Rd
man/MessinaResult-class.Rd
man/messina-package.Rd
man/messina.Rd
man/messinaDE.Rd
man/messinaSurv.Rd
man/messinaTopResults.Rd
man/plot-MessinaClassResult-missing-method.Rd
man/plot-MessinaSurvResult-missing-method.Rd
man/show-methods.Rd
man/tcga_kirc_example.Rd
src
src/Classifier.cpp
src/Classifier.h
src/Data.cpp
src/Data.h
src/RInterrupt.h
src/RcppExports.cpp
src/crossval.cpp
src/crossval.h
src/errors.cpp
src/errors.h
src/init.cpp
src/messinaExtern.cpp
src/types.h
vignettes
vignettes/messina.Rnw
messina documentation built on May 20, 2017, 9:27 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.