Identification of important regressor groups, subgroups and individuals via regularization methods

application to gut microbiome data

Tanya P. Garcia*, Samuel Müller, Raymond J. Carroll, Rosemary L. Walzem

*Corresponding author for this work

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

Motivation: 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.

Availability: The new approach is implemented in an R package, which is freely available from the corresponding author.

Original languageEnglish
Pages (from-to)831-837
Number of pages7
JournalBioinformatics
Volume30
Issue number6
DOIs
Publication statusPublished - 15 Mar 2014
Externally publishedYes

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