taxaPV: Calculate Proportional Variability For Taxa

In RIVM-IIV-Microbiome/biomeStats: Methods for carrying out association studies of the microbiome

Calculate Proportional Variability For Taxa

Description

Calculate Proportional Variability For Taxa

Usage

taxaPV(
  x,
  subsample = TRUE,
  lower_conf = 0.025,
  upper_conf = 0.975,
  sampling_n = 9,
  round_pv_vals = 3
)

Arguments

x	A phyloseq object
subsample	Logical. Default=TRUE.
lower_conf	Lower confidence. Default=0.025
upper_conf	Lower confidence. Default=0.975
sampling_n	Number of subsampling. Default=9
round_pv_vals	Return PV values by rounding to certain value. Default=3

Details

Proportional Variability of taxa using relative abundance. The Proportional Variability is a non-parametric measure of variability. https://doi.org/10.1371/journal.pone.0084074. Here, I have incorporated subsampling approach to quantify Proportional Variability in microbiome studies.

Value

A tibble with taxa ids, taxonomic information, two-group prevalence and fold change values.

Author(s)

Original Author: Leo Lahti. Adapted by Sudarshan A. Shetty

References

Heath JP, Borowski P. (2013). Quantifying Proportional Variability. PLoS ONE 8(12): e84074. https://doi.org/10.1371/journal.pone.0084074

Heath J. (2006) Quantifying temporal variability in population abundances. Oikos 115, no. 3 (2006): 573-581. https://doi.org/10.1111/j.2006.0030-1299.15067.x

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

Examples

library(biomeUtils)
library(dplyr)
library(microbiome)
data("FuentesIliGutData")
# Check for control samples how variable are core taxa
ps1 <- filterSampleData(FuentesIliGutData, ILI == "C") %>%
     microbiome::transform("compositional") %>%
     core(0.01, 75/100)
taxa_fd <- taxaPV(ps1)
taxa_fd

RIVM-IIV-Microbiome/biomeStats documentation built on Sept. 14, 2022, 5:15 p.m.