run_distance | R Documentation |
The function is to calculate the distance among samples
run_distance(
object,
level = c(NULL, "Kingdom", "Phylum", "Class",
"Order", "Family", "Genus",
"Species", "Strain", "unique"),
method = c("unifrac", "wunifrac", "GUniFrac", "bray", "dpcoa", "jsd"),
alpha = 0.5)
object |
(Required). a |
level |
(Optional). character. Summarization
level (from |
method |
(Required). character. Provide one of the currently supported
options. See
|
alpha |
(Optional). numeric. the parameter for "GUniFrac" controlling weight on abundant lineages (default: 0.5). |
distance object, which could be applied for ordination analysis.
Created by Hua Zou (5/14/2022 Shenzhen China)
## Not run:
# phyloseq object
data("Zeybel_2022_gut")
run_distance(Zeybel_2022_gut,
level = "Phylum",
method = "bray")
# SummarizedExperiment object
data("Zeybel_2022_protein")
run_distance(Zeybel_2022_protein,
method = "bray")
## End(Not run)
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