title: Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data.
abstract: BACKGROUND
  Gut microbiota can be classified at multiple taxonomy levels. Strategies to use changes in microbiota composition to effect health improvements require knowing at which taxonomy level interventions should be aimed. Identifying these important levels is difficult, however, because most statistical methods only consider when the microbiota are classified at one taxonomy level, not multiple.
  
  
  RESULTS
  Using L1 and L2 regularizations, we developed a new variable selection method that identifies important features at multiple taxonomy levels. The regularization parameters are chosen by a new, data-adaptive, repeated cross-validation approach, which performed well. In simulation studies, our method outperformed competing methods: it more often selected significant variables, and had small false discovery rates and acceptable false-positive rates. Applying our method to gut microbiota data, we found which taxonomic levels were most altered by specific interventions or physiological status.
  
  
  BACKGROUND
  The new approach is implemented in an R package, which is freely available from the corresponding author.
  
  
  BACKGROUND
  tpgarcia@srph.tamhsc.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Epidemiology & Biostatistics, School of Rural Public Health, Texas A&M Health Science Center, College Station, TX 77843-1266, USA, School of Mathematics and Statistics, University of Sydney, NSW 2006 Australia, Department of Statistics, Texas A&M University, College Station, TX 77843-3143, USA and Department of Poultry Science, Intercollegiate Faculty of Nutrition, Texas A&M University, College Station, TX 77840, USA.
authors.forename: Tanya P
authors.initials: TP
authors.lastname: Garcia
authors.forename: Samuel
authors.initials: S
authors.lastname: Müller
authors.forename: Raymond J
authors.initials: RJ
authors.lastname: Carroll
authors.forename: Rosemary L
authors.initials: RL
authors.lastname: Walzem
mesh_terms: D000818:Animals; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D051379:Mice; D064307:Microbiota; D012984:Software