comparePhyloseq: Compare Phyloseq Objects

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

Compare Phyloseq Objects

Description

Compare Phyloseq Objects

Usage

comparePhyloseq(x)

Arguments

x	A named list of phyloseq objects to compare

Details

Provided a named list of different phyloseq objects 'comparePhyloseq' returns a data.frame with basic values in each of the phyloseq objects.

Value

A tibble

Author(s)

Sudarshan A. Shetty

References

Shetty SA (2021). Utilities for microbiome analytics. https://github.com/RIVM-IIV-Microbiome/biomeUtils

Examples

library(biomeUtils)
data("FuentesIliGutData")
ps1 <- subset_samples(FuentesIliGutData, ILI == "C")
ps1 <- prune_taxa(taxa_sums(ps1) > 0, ps1)

ps2 <- subset_samples(FuentesIliGutData, ILI == "L1")
ps2 <- prune_taxa(taxa_sums(ps2) > 0, ps2)

ps3 <- subset_samples(FuentesIliGutData, ILI == "L2")
ps3 <- prune_taxa(taxa_sums(ps3) > 0, ps3)

ps.list <- c("C" = ps1, "L1" = ps2, "L2" = ps3)

comparePhyloseq(ps.list)

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