microbiome-baxter | R Documentation |
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
`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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