OKeefeDSData: Obtain the O'Keefe diet swap microbiome data

View source: R/OKeefeDSData.R

OKeefeDSDataR Documentation

Obtain the O'Keefe diet swap microbiome data


Obtain the microbiome data from O'Keefe et al. (2015).





The OKeefeDS dataset contains microbiome data from a study with African and African American groups undergoing a two-week diet swap.

This data set is based on the Human Intestinal Tract (HIT)Chip phylogenetic 16S microarray (Rajilic-Stojanovic et al. 2009. This profiling technology differs from the more widely used 16S rRNA amplicon sequencing.

Column metadata includes the subject identifier, sex, nationality, group information, sample identifier, time point information, time point information within group and BMI group.

Row metadata contains taxonomic information on the Phylum, Family and Genus level.

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


a TreeSummarizedExperiment


Felix G.M. Ernst and Leo Lahti


O'Keefe S et al. (2015): Fat, fibre and cancer risk in African Americans and rural Africans. Nature Communications 6:6342 (2015) https://dx.doi.org/10.1038/ncomms7342

Rajilic-Stojanovic M, Heilig HG, Molenaar D, Kajander K, Surakka A, Smidt H, de Vos WM (2009). Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol. 11(7):1736-51 https://doi.org/10.1111/j.1462-2920.2009.01900.x


tse <- OKeefeDSData()

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