microbiome-papa: Microbiome, Papa dataset results

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

Description

Results for case study on 16S microbiome differential testing of Papa et al. (2012) dataset described in Korthauer and Kimes et al. (2019). Wilcoxon rank-sum test was used to test for differential abundance between samples from patients with GI symptoms but not IBD, and IBD patients.

Arguments

metadata

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

Details

Results for this case study include:

• papa-genus-benchmark: testing at genus-level using ubiquity as covariate.

• papa-genus-abun-benchmark: testing at genus-level using mean abundance as covariate.

• papa-genus-log-ubiquity-benchmark: testing at genus-level using log-ubiquity as covariate.

• papa-genus-uninf-benchmark: testing at genus-level using uninformative covariate.

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

References

• Papa, E. et al. (2012). Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PloS One, 7(6), e39242.

See Also

microbiome-schubert, microbiome-baxter, microbiome-goodrich, microbiome-enigma

Examples

`papa-genus-benchmark`(metadata = TRUE)

## Not run: 
`papa-genus-benchmark`()
`papa-genus-abun-benchmark`()
`papa-genus-log-ubiquity-benchmark`()
`papa-genus-uninf-benchmark`()
`papa-otus-benchmark`()

## End(Not run)

stephaniehicks/benchmarkfdrData2019 documentation built on June 20, 2021, 10 a.m.