sCD14: sCD14 data

In jacobbien/trac: Tree-based Aggregation of Compositional Data

Description

This is the Gut (HIV) data used in Tree-Aggregated Predictive Modeling of Microbiome Data. This was processed based on a phyloseq object provided by Javier Rivera-Pinto. It is the BCN0 (Bacelona test dataset) from Gut Microbiota Linked to Sexual Preference and HIV Infection.

Usage

sCD14

Format

A named list:

y

Vector of n = 152 soluble CD14 levels in units of pg/ml

x

Matrix of fecal 16S rRNA amplicon data, with n = 152 rows corresponding to people and p = 539 columns corresponding to OTUs.

tree

Taxonomic tree of class phylo

tax

A data frame containing the taxonomic information for each OTU

A

A binary matrix encoding the tree structure with p = 539 rows, corresponding to leaves, and 626 columns, corresponding to all non-root nodes in the tree. See Tree-Aggregated Predictive Modeling of Microbiome Data for the definition of A.

jacobbien/trac documentation built on Oct. 18, 2021, 9:30 p.m.