FAMT

Package: FAMT
Type: Package
Title: Factor Analysis for Multiple Testing (FAMT) : simultaneous tests
under dependence in high-dimensional data
Version: 2.5
Date: 2013-09-30
Author: David Causeur, Chloe Friguet, Magalie Houee-Bigot, Maela Kloareg
Maintainer: David Causeur <David.Causeur@agrocampus-ouest.fr>
Depends: mnormt, impute
Description: The method proposed in this package takes into account the impact of dependence on the multiple testing procedures for high-throughput data as proposed by Friguet et al. (2009). The common information shared by all the variables is modeled by a factor analysis structure. The number of factors considered in the model is chosen to reduce the false discoveries variance in multiple tests. The model parameters are estimated thanks to an EM algorithm. Adjusted tests statistics are derived, as well as the associated p-values. The proportion of true null hypotheses (an important parameter when controlling the false discovery rate) is also estimated from the FAMT model. Graphics are proposed to interpret and describe the factors.
LazyLoad: yes
License: GPL (>= 2)
URL: http://famt.free.fr/
Packaged: 2014-01-02 14:02:18 UTC; ripley
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-01-02 15:15:13

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'FAMT' ...
** package 'FAMT' successfully unpacked and MD5 sums checked
** R
** data
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'FAMT'
    finding HTML links ... done
    FAMT-package                            html  
    annotations                             html  
    as.FAMTdata                             html  
    finding level-2 HTML links ... done

    covariates                              html  
    defacto                                 html  
    emfa                                    html  
    expression                              html  
    modelFAMT                               html  
    nbfactors                               html  
    pi0FAMT                                 html  
    raw.pvalues                             html  
    residualsFAMT                           html  
    summaryFAMT                             html  
** building package indices
** testing if installed package can be loaded
* DONE (FAMT)
Making 'packages.html' ... done