flan: An R Package for Inference on Mutation Models.

This paper describes flan, a package providing tools for fluctuation analysis of mutant cell counts. It includes functions dedicated to the distribution of final numbers of mutant cells. Parametric estimation and hypothesis testing are also implemented, enabling inference on different sorts of data with several possible methods. An overview of the subject is proposed. The general form of mutation models is described, including the classical models as particular cases. Estimating from a model, when the data have been generated by another, induces different possible biases, which are identified and discussed. The three estimation methods available in the package are described, and their mean squared errors are compared. Finally, implementation is discussed, and a few examples of usage on real data sets are given.

Adrien Mazoyer , Rémy Drouilhet , Stéphane Despréaux , Bernard Ycart

CRAN packages used

flan, Rcpp, ggplot2, RcppGSL, polynom, RcppArmadillo, lbfgsb3

CRAN Task Views implied by cited packages

NumericalMathematics, Graphics, HighPerformanceComputing, Optimization, Phylogenetics


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For attribution, please cite this work as

Mazoyer, et al., "The R Journal: flan: An R Package for Inference on Mutation Models.", The R Journal, 2017

BibTeX citation

  author = {Mazoyer, Adrien and Drouilhet, Rémy and Despréaux, Stéphane and Ycart, Bernard},
  title = {The R Journal: flan: An R Package for Inference on Mutation Models.},
  journal = {The R Journal},
  year = {2017},
  note = {https://doi.org/10.32614/RJ-2017-029},
  doi = {10.32614/RJ-2017-029},
  volume = {9},
  issue = {1},
  issn = {2073-4859},
  pages = {334-351}