Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data.
Bioinformatics
; 30(6): 831-7, 2014 Mar 15.
Article
in En
| MEDLINE
| ID: mdl-24162467
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. CONTACT: tpgarcia@srph.tamhsc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Full text:
1
Database:
MEDLINE
Main subject:
Gastrointestinal Tract
/
Microbiota
Type of study:
Diagnostic_studies
/
Prognostic_studies
Limits:
Animals
/
Humans
Language:
En
Journal:
Bioinformatics
Journal subject:
INFORMATICA MEDICA
Year:
2014
Type:
Article
Affiliation country:
United States