alpha_div_calc: Alpha diversity
In ericjcgalvez/MicrobiomeWrangler:
View source: R/alpha_diver_fun.R
alpha_div_calc R Documentation
Alpha diversity
Description
Calulates alpha diversity distances
Usage
alpha_div_calc(
phylo,
min_count = 2000,
measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson",
"BF_ratio")
)
Arguments
phylo
reads a phyloseq object
min_count
samples that do not reach this count number
measures
character vector. Type of alpha diversity indexes. Possible
values: c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson",
"BF_ratio"). "BF_ratio" calculates the ratio of Bacteroidetes and Firmicutes.
Examples
data("mice_B6_N")
alpha_diversity_plus_dt(mice_B6_N, 2000)
ericjcgalvez/MicrobiomeWrangler documentation built on April 14, 2022, 6:33 p.m.
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View source: R/alpha_diver_fun.R
| alpha_div_calc | R Documentation |
Alpha diversity
Description
Calulates alpha diversity distances
Usage
alpha_div_calc(
phylo,
min_count = 2000,
measures = c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson",
"BF_ratio")
)
Arguments
phylo |
reads a phyloseq object |
min_count |
samples that do not reach this count number |
measures |
character vector. Type of alpha diversity indexes. Possible values: c("Observed", "Chao1", "ACE", "Shannon", "Simpson", "InvSimpson", "BF_ratio"). "BF_ratio" calculates the ratio of Bacteroidetes and Firmicutes. |
Examples
data("mice_B6_N")
alpha_diversity_plus_dt(mice_B6_N, 2000)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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