getTaxaSummary: Get Taxa Summary at Specific Taxonomic Level

In RIVM-IIV-Microbiome/biomeUtils: Utilities for microbiome analytics

Get Taxa Summary at Specific Taxonomic Level

Description

Get Taxa Summary at Specific Taxonomic Level

Usage

getTaxaSummary(x, rank = "Phylum")

Arguments

x	A phyloseq object
rank	Taxonomic rank for which abundance summaries are required.

Details

Get a summary of total abundances of taxa at specific taxonomic level.

Author(s)

Sudarshan A. Shetty

References

Shetty SA (2020). Utilities for microbiome analytics. https://github.com/RIVM-IIV-Microbiome/biomeUtils

See Also

getTaxaSummary

Examples

library(biomeUtils)
library(dplyr)
data("SprockettTHData")
x <- subset_samples(SprockettTHData,
                    Delivery_Mode=="Vaginal" & Cohort == "Tsimane")
x <- removeZeros(x)
getTaxaSummary(x, rank="Phylum")

RIVM-IIV-Microbiome/biomeUtils documentation built on July 20, 2023, 10:29 a.m.