microbiome-schubert: Microbiome, Schubert dataset results

In stephaniehicks/benchmarkfdrData2019: Data and Benchmarking Results from Korthauer and Kimes et al. (2019)

Microbiome, Schubert dataset results

Description

Results for case study on 16S microbiome differential testing of Schubert et al. (2014) dataset described in Korthauer and Kimes et al. (2019). Wilcoxon rank-sum test was used to test for differential abundance between samples from healthy patients and patients with diarrheal stool samples (including both C. difficile infection, CDI, and non-CDI samples).

Arguments

metadata

logical whether to load metadata (TRUE) or full resource (FALSE). (default = FALSE)

Details

Results for this case study include:

• schubert-otus-benchmark: testing at OTU-level using ubiquity as covariate.

• schubert-otus-abun-benchmark: testing at OTU-level using mean abundance as covariate.

• schubert-otus-uninf-benchmark: testing at OTU-level using uninformative covariate.

References

• Schubert, A. M. et al. (2014). Microbiome data distinguish patients with Clostridium difficile infection and non-C. difficile-associated diarrhea from healthy controls. MBio, 5(3), e01021-14.

See Also

microbiome-baxter, microbiome-goodrich, microbiome-papa, microbiome-enigma

Examples

`schubert-otus-benchmark`(metadata = TRUE)

## Not run: 
`schubert-otus-benchmark`()
`schubert-otus-abun-benchmark`()
`schubert-otus-uninf-benchmark`()

## End(Not run)

stephaniehicks/benchmarkfdrData2019 documentation built on April 13, 2025, 9:02 p.m.