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

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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.

Author
David Causeur, Chloe Friguet, Magalie Houee-Bigot, Maela Kloareg
Date of publication
2014-01-02 15:15:13
Maintainer
David Causeur <David.Causeur@agrocampus-ouest.fr>
License
GPL (>= 2)
Version
2.5
URLs

View on CRAN

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

Files in this package

FAMT
FAMT/NAMESPACE
FAMT/data
FAMT/data/covariates.rda
FAMT/data/expression.rda
FAMT/data/annotations.rda
FAMT/data/datalist
FAMT/R
FAMT/R/raw.pvalues.R
FAMT/R/pi0FAMT.R
FAMT/R/summaryFAMT.R
FAMT/R/defacto.R
FAMT/R/modelFAMT.R
FAMT/R/nbfactors.R
FAMT/R/residualsFAMT.R
FAMT/R/as.FAMTdata.R
FAMT/R/emfa.R
FAMT/R/FAMT_2.5-internal.R
FAMT/MD5
FAMT/DESCRIPTION
FAMT/man
FAMT/man/summaryFAMT.Rd
FAMT/man/expression.Rd
FAMT/man/pi0FAMT.Rd
FAMT/man/as.FAMTdata.Rd
FAMT/man/annotations.Rd
FAMT/man/FAMT-package.Rd
FAMT/man/modelFAMT.Rd
FAMT/man/residualsFAMT.Rd
FAMT/man/emfa.Rd
FAMT/man/defacto.Rd
FAMT/man/raw.pvalues.Rd
FAMT/man/covariates.Rd
FAMT/man/nbfactors.Rd