SigCheck

Package: SigCheck
Type: Package
Title: Check a gene signature's prognostic performance against random
signatures, known signatures, and permuted data/metadata
Version: 2.4.0
Author: Rory Stark <rory.stark@cruk.cam.ac.uk> and
Justin Norden
Maintainer: Rory Stark <rory.stark@cruk.cam.ac.uk>
Description: 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.
License: Artistic-2.0
LazyLoad: yes
Depends: R (>= 3.2.0), MLInterfaces, Biobase, e1071, BiocParallel,
survival
Imports: graphics, stats, utils, methods
Suggests: BiocStyle, breastCancerNKI, qusage
biocViews: GeneExpression, Classification, GeneSetEnrichment
NeedsCompilation: no
Packaged: 2016-05-04 05:51:45 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'SigCheck' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'signature' in package 'SigCheck'
** help
*** installing help indices
  converting help for package 'SigCheck'
    finding HTML links ... done
    SigCheck-package                        html  
    finding level-2 HTML links ... done

    SigCheckObject-class                    html  
    classifyResults                         html  
    knownSignatures                         html  
    nkiResults                              html  
    sigCheck                                html  
    sigCheckAll                             html  
    sigCheckKnown                           html  
    sigCheckPermuted                        html  
    sigCheckPlot                            html  
    sigCheckRandom                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (SigCheck)
Making 'packages.html' ... done