To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SigCheck")

In most cases, you don't need to download the package archive at all.

SigCheck

   

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see SigCheck.

Check a gene signature's classification performance against random signatures, permuted data, and known signatures.

Bioconductor version: 3.0

While gene signatures are frequently used to classify data (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 partly on suggestions in that paper, SigCheck accepts a data set (as an ExpressionSet) and a gene signature, and compares its classification performance (using the MLInterfaces package) against a) random gene signatures of the same length; b) known, (related and unrelated) gene signatures; and c) permuted data.

Author: Justin Norden <jn333 at cam.ac.uk> and Rory Stark <rory.stark at cruk.cam.ac.uk>

Maintainer: Rory Stark <rory.stark at cruk.cam.ac.uk>

Citation (from within R, enter citation("SigCheck")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("SigCheck")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("SigCheck")

 

PDF R Script Checking gene expression signatures against random and known signatures with SigCheck
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, GeneExpression, GeneSetEnrichment, Software
Version 1.0.2
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License Artistic-2.0
Depends R (>= 3.1.0), MLInterfaces, Biobase, e1071, BiocParallel
Imports graphics, stats, utils
LinkingTo
Suggests BiocStyle, breastCancerNKI
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Package Source SigCheck_1.0.2.tar.gz
Windows Binary SigCheck_1.0.2.zip
Mac OS X 10.6 (Snow Leopard) SigCheck_1.0.2.tgz
Mac OS X 10.9 (Mavericks) SigCheck_1.0.2.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/SigCheck/tree/release-3.0
Package Short Url http://bioconductor.org/packages/SigCheck/
Package Downloads Report Download Stats

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