HintikkaXOData: Retrieve HintikkaXO data

In microbiome/microbiomeDataSets: Experiment Hub based microbiome datasets

Retrieve HintikkaXO data

Description

Obtain microbiota, metabolite and biomarker data from Hintikka et al. (2021).

Usage

HintikkaXOData()

Details

The HintikkaXO dataset contains high-throughput profiling data from 40 rat samples, including 39 biomarkers, 38 metabolites (NMR), and 12706 OTUs from 318 species, measured from Cecum. This is diet comparison study with High/Low fat diet and xylo-oligosaccaride supplementation.

Column metadata is common for all experiments (microbiota, metabolites, biomarkers) and includes the following fields:

• Sample: Sample ID (character)

• Rat: Rat ID (factor)

• Site: Site of measurement ("Cecum"); single value

• Diet: Diet group (factor; combination of the Fat and XOS fields)

• Fat: Fat in Diet (factor; Low/High)

• XOS: XOS Diet Supplement (numeric; 0/1)

Row metadata of the microbiota data contains taxonomic information on the Phylum, Class, Order, Family, Genus, Species, and OTU levels.

Biomarker data contains 39 biomarkers.

Metabolite data contains 38 NMR metabolites.

All data are downloaded from ExperimentHub and cached for local re-use.

Value

for HintikkaXOData a MultiAssayExperiment is provided.

Author(s)

Leo Lahti

References

Hintikka L et al. (2021): Xylo-oligosaccharides in prevention of hepatic steatosis and adipose tissue inflammation: associating taxonomic and metabolomic patterns in fecal microbiotas with biclustering. International Journal of Environmental Research and Public Health 18(8):4049 https://doi.org/10.3390/ijerph18084049

Examples

# Retrieve the MAE data
mae <- HintikkaXOData()

# List the experiments in this MultiAssayExperiment object
print(experiments(mae))

# colData for this MAE data object (print first few rows)
print(head(colData(mae)))

# metabolite assay data
nmr <- assays(mae[["metabolites"]])$nmr

# biomarker assay data
bm <- assays(mae[["biomarkers"]])$signals
# microbiota assay counts
counts <- assays(mae[["microbiota"]])$counts

# microbiota rowData
taxtab <- rowData(mae[["microbiota"]])

microbiome/microbiomeDataSets documentation built on July 31, 2022, 6:09 a.m.