FAMT: Factor Analysis for Multiple Testing (FAMT) : simultaneous tests under dependence in high-dimensional data
Version 2.5

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.

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AuthorDavid Causeur, Chloe Friguet, Magalie Houee-Bigot, Maela Kloareg
Date of publication2014-01-02 15:15:13
MaintainerDavid Causeur <David.Causeur@agrocampus-ouest.fr>
LicenseGPL (>= 2)
Version2.5
URL http://famt.free.fr/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("FAMT")

Man pages

annotations: Gene annotations data frame
as.FAMTdata: Create a 'FAMTdata' object from an expression, covariates and...
covariates: Covariates data frame
defacto: FAMT factors description
emfa: Factor Analysis model adjustment with the EM algorithm
expression: Gene expressions data frame
FAMT-package: Factor Analysis for Multiple Testing (FAMT) : simultaneous...
modelFAMT: The FAMT complete multiple testing procedure
nbfactors: Estimation of the optimal number of factors of the FA model
pi0FAMT: Estimation of the Proportion of True Null Hypotheses
raw.pvalues: Calculation of classical multiple testing statistics and...
residualsFAMT: Calculation of residual under null hypothesis
summaryFAMT: Summary of a FAMTdata or a FAMTmodel

Functions

FAMT Man page
FAMT-package Man page
annotations Man page
as.FAMTdata Man page Source code
covariates Man page
defacto Man page Source code
emfa Man page Source code
expression Man page
modelFAMT Man page Source code
nbfactors Man page Source code
pi0FAMT Man page Source code
raw.pvalues Man page Source code
residualsFAMT Man page Source code
summaryFAMT Man page Source code

Files

NAMESPACE
data
data/covariates.rda
data/expression.rda
data/annotations.rda
data/datalist
R
R/raw.pvalues.R
R/pi0FAMT.R
R/summaryFAMT.R
R/defacto.R
R/modelFAMT.R
R/nbfactors.R
R/residualsFAMT.R
R/as.FAMTdata.R
R/emfa.R
R/FAMT_2.5-internal.R
MD5
DESCRIPTION
man
man/summaryFAMT.Rd
man/expression.Rd
man/pi0FAMT.Rd
man/as.FAMTdata.Rd
man/annotations.Rd
man/FAMT-package.Rd
man/modelFAMT.Rd
man/residualsFAMT.Rd
man/emfa.Rd
man/defacto.Rd
man/raw.pvalues.Rd
man/covariates.Rd
man/nbfactors.Rd
FAMT documentation built on May 19, 2017, 6:55 p.m.