phy: A phyloseq-class experiment-level object example data.

In JiyuanHu/massMap: massMap: a two-stage microbial association mapping framework with advanced FDR control

Description

This data is a phyloseq-class object which contains the OTU table, sample data, taxonomy table and phylogenetic tree information. Details about the phyloseq class please see the R package "phyloseq". We are interested in the association between microbial taxa and the binary outcome trait antibiotic history (ABH) adjusting for age and gender.

Usage

data(phy)

Format

phyloseq-class experiment-level object

otu_table()

OTU Table: [ 90 taxa and 100 samples ]

..@ .Data: a matrix where each row represents the suject,each column represents the OTU.

..@ taxa_are_rows: logi FALSE

sample_data()

Sample Data: [ 100 samples by 3 sample variables ]

A data frame with 100 observations for one outcome variable ABH and two covariates age and gender.

ABH: a numeric vector indicating the antibiotic history of each individual, where ABH =0 indicating the individual without antibiotic usage and ABH=1 indicating the individual having antibiotic usage in the preceding year;

age: a numeric vector;

gender: a factor with levels female, male.

tax_table()

Taxonomy Table: [ 90 taxa by 7 taxonomic ranks ]

..@ .Data: a matrix where each row represents the taxonomy alignment on Kingdom (Domain), Phylum, Class, Order, Family, Genus and Species represently for each taxon.

phy_tree()

Phylogenetic Tree: [ 90 tips and 89 internal nodes ]

The phylogenetic tree of the example microbiome data. Look for details in the help file of phy_tree() from "phyloseq" package.

JiyuanHu/massMap documentation built on May 26, 2020, 2:20 a.m.