% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/mia.R
\docType{data}
\name{ibdmdb}
\alias{ibdmdb}
\title{IBDMDB 2-omic demo dataset (MGX + MTX)}
\format{
A \code{MultiAssayExperiment} with two experiments:
\describe{
\item{se_mgx}{A \code{SummarizedExperiment} with MGX abundance data.}
\item{se_mtx}{A \code{SummarizedExperiment} with MTX abundance data.}
\item{mae2}{A \code{MultiAssayExperiment} containing both experiments.}
}
}
\source{
Prepared by \code{inst/scripts/prepare_ibdmdb_demo.R}. The script is for
developers and downloads publicly available IBDMDB/HMP2 taxonomic profiles
and metadata from Zenodo into a local cache (e.g. \code{tools/cache/}),
then subsets and filters the raw data to create a small example suitable
for vignettes.
}
\usage{
data("ibdmdb")
}
\description{
A compact example derived from the Integrative Human Microbiome Project (iHMP)
Inflammatory Bowel Disease (IBD) cohort.
}
\details{
The dataset \code{ibdmdb} is a named list with:
\itemize{
\item \code{se_mgx}: metagenomic taxonomic profiles (MGX)
\item \code{se_mtx}: metatranscriptomic taxonomic profiles (MTX)
\item \code{mae2}: a \link[MultiAssayExperiment]{MultiAssayExperiment}
containing both experiments
}

These compact objects are intended for quick examples and vignettes.
Load with:
\code{data("ibdmdb")}.
}
\references{
Lloyd-Price J, Arze C, Ananthakrishnan AN, et al.
\emph{Multi-omics of the gut microbial ecosystem in inflammatory bowel
diseases.}
Nature 569, 655–662 (2019).
\doi{10.1038/s41586-019-1237-9}
}
\keyword{datasets}
