IBDMDB 2-omic demo dataset (MGX + MTX)

Source: R/mia.R

A compact example derived from the Integrative Human Microbiome Project (iHMP) Inflammatory Bowel Disease (IBD) cohort.

data("ibdmdb_2omic_demo")

Format

A MultiAssayExperiment with two experiments:

se_mgx

A SummarizedExperiment with MGX abundance data.

se_mtx

A SummarizedExperiment with MTX abundance data.

mae2

A MultiAssayExperiment containing both experiments.

Source

Prepared by 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. tools/cache/), then subsets and filters the raw data to create a small example suitable for vignettes.

Details

The dataset ibdmdb_2omic_demo is a named list with:

  • se_mgx: metagenomic taxonomic profiles (MGX)

  • se_mtx: metatranscriptomic taxonomic profiles (MTX)

  • mae2: a MultiAssayExperiment containing both experiments

These compact objects are intended for quick examples and vignettes. Load with: data("ibdmdb_2omic_demo").

References

Lloyd-Price J, Arze C, Ananthakrishnan AN, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655–662 (2019). doi:10.1038/s41586-019-1237-9