Author: David Causeur, Chloe Friguet, Magalie Houee-Bigot, Maela Kloareg
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.

Title: Factor Analysis for Multiple Testing (FAMT) : Simultaneous Tests
under Dependence in High-Dimensional Data

Description: Fatty Acid Metabolic Analysis aimed to the estimation of FA import (I), de novo synthesis (S), fractional contribution of the 13C-tracers (D0, D1, D2), elongation (E) and desaturation (Des) based on mass isotopologue data.
Depends: R (>= 4.0), LipidMS, rmarkdown, knitr
Imports: accucor, scales, gtools, minpack.lm, tidyr, plyr, gplots,
Author: Maribel Alcoriza-Balaguer [aut, cre],

Description: Fatty acid metabolic analysis aimed to the estimation of FA import (I), de novo synthesis (S), fractional contribution of the 13C-tracers (D0, D1, D2), elongation (E) and desaturation (Des) based on mass isotopologue data.

Title: A Flexible Algorithm for Model Selection (FAMoS)
Description: Given a set of parameters describing model dynamics and a corresponding cost function,
FAMoS attempts to find the most suitable parameter subset in terms of a specified information
criterion. Works on any cost function that returns a negative log-likelihood.

Title: A Flexible Algorithm for Model Selection
FAMoS performs a dynamic forward-backward model selection on a specified selection
criterion. It also applies a non-local swap search method. Works on any cost function.