genericUtilities: Generic utilities

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

Generic utilities

Description

Generic utilities

Usage

meltAbundance(x, ...)

transposeAbundance(x, transform = "identity")

Arguments

x	phyloseq object
...	Arguments other than 'cols' to pass to tidyr pivot_longer function
transform	If transformation is required 'transposeAbundance'

Details

Generic utilities that are simple wrappers for doing common tasks.

meltAbundance convert abundance data to long format.

transposeAbundance transpose OTU for use with vegan pkg.

Value

long data format.

Author(s)

Sudarshan A. Shetty

References

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

Examples

library(biomeUtils)
data("FuentesIliGutData")
melt.abund <- meltAbundance(FuentesIliGutData,
                            names_to = "SampleID",
                            values_to="Abundance")
melt.abund

t.otu <- transposeAbundance(FuentesIliGutData)
dim(t.otu)

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