collapse_taxonomy: Collapse taxonomy into single strings
In AlmaasLab/micInt: Find microbial interactions
View source: R/data_refinement.R
collapse_taxonomy R Documentation
Collapse taxonomy into single strings
Description
Given a phyloseq object with a taxonomy table, this function extracts the taxonomy of each OTU and
collapse the result into a single string
Usage
collapse_taxonomy(phyloseq)
Arguments
phyloseq
A phyloseq object containing the tax_table slot. If this slot does not exist,
the function will return NULL.
Value
A named character vector, where the names are the OTU names and the values are the collapsed taxonomies.
Examples
library(micInt)
collapsed <- collapse_taxonomy(seawater)
collapsed
AlmaasLab/micInt documentation built on April 1, 2022, 10:37 a.m.
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View source: R/data_refinement.R
| collapse_taxonomy | R Documentation |
Collapse taxonomy into single strings
Description
Given a phyloseq object with a taxonomy table, this function extracts the taxonomy of each OTU and collapse the result into a single string
Usage
collapse_taxonomy(phyloseq)
Arguments
phyloseq |
A |
Value
A named character vector, where the names are the OTU names and the values are the collapsed taxonomies.
Examples
library(micInt) collapsed <- collapse_taxonomy(seawater) collapsed
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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