checkFilterEffect: Check Filter Effect

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

Check Filter Effect

Description

Check Filter Effect

Usage

checkAbundanceCutOffs(x, abundance_thres = NULL, prevalence_thres = NULL)

checkPrevalenceCutOffs(x, abundance_thres = NULL, prevalence_thres = NULL)

Arguments

x	phyloseq object
abundance_thres	If using 'checkAbundanceCutOffs', can have multiple numeric values like c(0.1, 0.01, 0.001, 0.0001). If using 'checkPrevalenceCutOffs', a single value.
prevalence_thres	If using 'checkPrevalenceCutOffs', can have multiple numeric values like c(0.05, 0.1, 0.15, 0.2). If using 'checkAbundanceCutOffs', a single value.

Details

Investigate effect of abundance and prevalence thresholds on taxa numbers.

checkAbundanceCutOffs check how many taxa are lost at different abundance thresholds.

checkPrevalenceCutOffs check how many taxa are lost at different prevalence thresholds.

Value

A tibble

Author(s)

Sudarshan A. Shetty

References

Shetty SA (2020). Utilities for microbiome analytics. https://github.com/microsud/biomeUtils

Examples

library(biomeUtils)
library(microbiome)
data("FuentesIliGutData")
ps.rel <- microbiome::transform(FuentesIliGutData, "compositional")
ab.check <- checkAbundanceCutOffs(ps.rel,
                                  abundance_thres = c(0.0001, 0.001, 0.01, 0.1),
                                  prevalence_thres = 0.1)
ab.check

pv.check <- checkPrevalenceCutOffs(ps.rel,
                                   abundance_thres = 0.01,
                                   prevalence_thres = c(0.05, 0.1, 0.15, 0.2))
pv.check

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