themetagenomics (version 1.0.2)

GEVERS: Inflammatory bowel disease gut microbiome data

Description

Subset of samples from the 16S amplicon Gevers et al pediatric inflammatory bowel disease (IBD) dataset. The data include 200 gut samples, 100 of which are controls, spanning 991 OTUs. Three tables are included: an OTU table generated via QIIME, picked against GreenGreens 13.5 at 97 similarity; a taxonomy reference table, and a sample metadata table that includes diagnosis and PCDAI scores, a continuous measure of disease burden.

Usage

GEVERS

Format

A list containing a 200x991 matrix (OTU), a 991x7 matrix (TAX), and a 200x3 dataframe (META).

References

Gevers, D., Kugathasan, S., Denson, L.A., et al. (2014). The Treatment-Naive Microbiome in New-Onset Crohn<U+2019>s Disease. Cell Host Microbe 15, 382<U+2013>392. (PubMed)

Examples

# NOT RUN {
hist(log(GEVERS$OTU + 1),100)
table(GEVERS$META$DIAGNOSIS)
boxplot(subset(GEVERS$META,DIAGNOSIS == 'CD')[['PCDAI']])
# }