pullPhyloseq: Pull Information from Phyloseq Object

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

Pull Information from Phyloseq Object

Description

Pull Information from Phyloseq Object

Usage

pullSampleAbundance(x, ...)

pullTaxaAbundance(x, ...)

pullTaxaRank(x, ...)

Arguments

x	phyloseq object
...	Option to pass on to pull. Only when using filterSampleData or filterTaxaData sample data or taxonomy table as tibble.

Details

These are alternative to subset and prune functions in phyloseq.

The pullSampleAbundance can be used to get abundances of all taxa.

The pullTaxaAbundance can be used to get abundances of a taxa in all samples.

The pullSampleVariable can be used to get all variables within a column in sample_data.

The pullTaxaRank can be used to get all taxomic information at a particular rank in tax_table.

The naming is using pull because it uses the dplyr::pull function.

Value

A vector of requested value

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")
pullSampleAbundance(FuentesIliGutData, "sample_1", name= "FeatureID")

pullTaxaAbundance(FuentesIliGutData, "ASV1", name = "SampleID")

pullTaxaRank(FuentesIliGutData, "Genus")

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