Open AccessStatistical Object Data Analysis of Taxonomic Trees from Human Microbiome Data
Author(s) -
Patricio S. La Rosa,
Berkley Shands,
Elena Deych,
Yanjiao Zhou,
Erica Sodergren,
George M. Weinstock,
William D. Shan
Publication year - 2012
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0048996
Subject(s) - human microbiome project , statistical inference , microbiome , computer science , inference , metagenomics , statistical model , set (abstract data type) , data set , tree (set theory) , data mining , object (grammar) , parametric statistics , artificial intelligence , human microbiome , machine learning , statistics , biology , mathematics , bioinformatics , mathematical analysis , biochemistry , gene , programming language
Human microbiome research characterizes the microbial content of samples from human habitats to learn how interactions between bacteria and their host might impact human health. In this work a novel parametric statistical inference method based on object-oriented data analysis (OODA) for analyzing HMP data is proposed. OODA is an emerging area of statistical inference where the goal is to apply statistical methods to objects such as functions, images, and graphs or trees. The data objects that pertain to this work are taxonomic trees of bacteria built from analysis of 16S rRNA gene sequences (e.g. using RDP); there is one such object for each biological sample analyzed. Our goal is to model and formally compare a set of trees. The contribution of our work is threefold: first, a weighted tree structure to analyze RDP data is introduced; second, using a probability measure to model a set of taxonomic trees, we introduce an approximate MLE procedure for estimating model parameters and we derive LRT statistics for comparing the distributions of two metagenomic populations; and third the Jumpstart HMP data is analyzed using the proposed model providing novel insights and future directions of analysis.