microbiome-papa | R Documentation |
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.
metadata |
logical whether to load metadata (TRUE) or full resource (FALSE). (default = FALSE) |
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.
Papa, E. et al. (2012). Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PloS One, 7(6), e39242.
microbiome-schubert
, microbiome-baxter
, microbiome-goodrich
, microbiome-enigma
`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)
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