prepTaxaAbundanceData: Prepares Taxa Abundance Data for Association analysis

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

Prepares Taxa Abundance Data for Association analysis

Description

Prepares Taxa Abundance Data for Association analysis

Usage

prepTaxaAbundanceData(
  x,
  detection_threshold = 0.001,
  prevalence_threshold = 5/100
)

Arguments

x	phyloseq-class object
detection_threshold	Remove taxa with less than this abundance in total dataset
prevalence_threshold	Remove taxa with less than this prevalence in total dataset

Details

Prepares the phyloseq-class object to taxa abundance table for check associations

Value

A tibble

Author(s)

Sudarshan A. Shetty

References

Ferreira JA, Fuentes S. (2020). Some comments on certain statistical aspects of the study of the microbiome. Briefings in bioinformatics 21(4), pp.1487-1494. https://doi.org/10.1093/bib/bbz077

Examples

library(biomeStats)
data("FuentesIliGutData")
ps <- FuentesIliGutData
gen_tab <- prepTaxaAbundanceData(ps,
                        detection_threshold = 0.01,
                        prevalence_threshold = 10/100)
head(gen_tab)

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