Description Arguments Details References See Also Examples
Results for case study on 16S microbiome differential testing of Baxter et al. (2016) 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 colorectal cancer and patients with no colonic lesions.
metadata |
logical whether to load metadata (TRUE) or full resource (FALSE). (default = FALSE) |
Results for this case study include:
baxter-genus-benchmark
: testing at genus-level using ubiquity as covariate.
baxter-genus-log-ubiquity-benchmark
: testing at genus-level using log-ubiquity as covariate.
baxter-genus-mean-abun-benchmark
: testing at genus-level using mean abundance as covariate.
baxter-genus-mean-uninf-benchmark
: testing at genus-level using uninformative covariate.
baxter-otus-benchmark
: testing at OTU-level using ubiquity as covariate.
baxter-otus-log-ubiquity-benchmark
: testing at OTU-level using log-ubiquity as covariate.
Baxter, N. T., Ruffin, M. T., Rogers, M. A., & Schloss, P. D. (2016). Microbiota-based model improves the sensitivity of fecal immunochemical test for detecting colonic lesions. Genome Medicine, 8(1), 37.
microbiome-schubert
, microbiome-goodrich
, microbiome-papa
, microbiome-enigma
1 2 3 4 5 6 7 8 9 10 11 | `baxter-genus-benchmark`(metadata = TRUE)
## Not run:
`baxter-genus-benchmark`()
`baxter-genus-log-ubiquity-benchmark`()
`baxter-genus-mean-abun-benchmark`()
`baxter-genus-mean-uninf-benchmark`()
`baxter-otus-benchmark`()
`baxter-otus-log-ubiquity-benchmark`()
## End(Not run)
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