SigCheck: Check a gene signature's prognostic performance against random signatures, known signatures, and permuted data/metadata

While gene signatures are frequently used to predict phenotypes (e.g. predict prognosis of cancer patients), it it not always clear how optimal or meaningful they are (cf David Venet, Jacques E. Dumont, and Vincent Detours' paper "Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome"). Based on suggestions in that paper, SigCheck accepts a data set (as an ExpressionSet) and a gene signature, and compares its performance on survival and/or classification tasks against a) random gene signatures of the same length; b) known, related and unrelated gene signatures; and c) permuted data and/or metadata.

AuthorRory Stark <rory.stark@cruk.cam.ac.uk> and Justin Norden
Date of publicationNone
MaintainerRory Stark <rory.stark@cruk.cam.ac.uk>
LicenseArtistic-2.0
Version2.6.0

View on Bioconductor

Functions

annotation,SigCheckObject-method Man page
checkType,SigCheckObject-method Man page
classes,SigCheckObject-method Man page
classifierMethod,SigCheckObject-method Man page
classifier,SigCheckObject-method Man page
classifyResults Man page
confusion,SigCheckObject-method Man page
knownSignatures Man page
modePerformance,SigCheckObject-method Man page
modeVal,SigCheckObject-method Man page
nkiResults Man page
resultsNKI Man page
sigCheck Man page
SigCheck Man page
sigCheckAll Man page
sigCheckKnown Man page
SigCheckObject Man page
SigCheckObject-class Man page
SigCheck-package Man page
sigCheckPermuted Man page
sigCheckPlot Man page
sigCheckRandom Man page
signature,SigCheckObject-method Man page
sigPerformance,SigCheckObject-method Man page
survivalClassificationScore,SigCheckObject-method Man page
survivalConfusionMatrix,SigCheckObject-method Man page
survivalMethod,SigCheckObject-method Man page
survivalPval,SigCheckObject-method Man page
survivalScores,SigCheckObject-method Man page
survival,SigCheckObject-method Man page
survivalTrainingClassificationScore,SigCheckObject-method Man page
survivalTrainingConfusionMatrix,SigCheckObject-method Man page
survivalTrainingPval,SigCheckObject-method Man page
survivalTrainingScores,SigCheckObject-method Man page
survivalType,SigCheckObject-method Man page
threshold,SigCheckObject-method Man page
timeUnits,SigCheckObject-method Man page
validationSamples,SigCheckObject-method Man page

Files

SigCheck/DESCRIPTION
SigCheck/NAMESPACE
SigCheck/R
SigCheck/R/SigCheck-class.R SigCheck/R/sigCheck.R SigCheck/R/sigCheckClassifier.R SigCheck/R/sigCheckKnown.R SigCheck/R/sigCheckPermuted.R SigCheck/R/sigCheckPlot.R SigCheck/R/sigCheckRandom.R SigCheck/R/sigCheckSurvival.R
SigCheck/build
SigCheck/build/vignette.rds
SigCheck/data
SigCheck/data/classifyResults.RData
SigCheck/data/datalist
SigCheck/data/knownSignatures.RData
SigCheck/data/nkiResults.RData
SigCheck/inst
SigCheck/inst/NEWS.Rd
SigCheck/inst/doc
SigCheck/inst/doc/SigCheck.R
SigCheck/inst/doc/SigCheck.Rnw
SigCheck/inst/doc/SigCheck.pdf
SigCheck/man
SigCheck/man/SigCheck-package.Rd SigCheck/man/SigCheckObject-class.Rd SigCheck/man/classifyResults.Rd SigCheck/man/knownSignatures.Rd SigCheck/man/nkiResults.Rd SigCheck/man/sigCheck.Rd SigCheck/man/sigCheckAll.Rd SigCheck/man/sigCheckKnown.Rd SigCheck/man/sigCheckPermuted.Rd SigCheck/man/sigCheckPlot.Rd SigCheck/man/sigCheckRandom.Rd
SigCheck/vignettes
SigCheck/vignettes/SigCheck.Rnw
SigCheck/vignettes/SigCheck.bib

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

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

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