getPhyloseqSlots: Get Phyloseq slots from Tibbles

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

Get Phyloseq slots from Tibbles

Description

Get Phyloseq slots from Tibbles

Usage

getOtuTableFromTibble(x, rownames = "FeatureID")

getTaxaTableFromTibble(x, rownames = "FeatureID")

getSampleTableFromTibble(x, rownames = NULL)

Arguments

x	phyloseq object
rownames	A column in tibble to use are rownames

Details

Convert different tibbles into phyloseq slots.

getOtuTableFromTibble Converts OTU tibble obtained using biomeUtils::getAbundanceTibble to phyloseq::otu_table.

getTaxaTableFromTibble Converts the taxa tibble obtained using biomeUtils::getTaxaTibble to phyloseq::tax_table.

getSampleTableFromTibble Converts the sample data tibble obtained using biomeUtils::getSampleTibble to phyloseq::sample_data.

Value

Either otu_table or tax_table or sample_data

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")
otu_tib  <- getAbundanceTibble(FuentesIliGutData)
otu_table <- getOtuTableFromTibble(otu_tib, rownames="FeatureID")
class(otu_table)

tax_tib <- getTaxaTibble(FuentesIliGutData)
taxa_table <- getTaxaTableFromTibble(tax_tib, rownames="FeatureID")
class(tax_table)

meta_tib <- getSampleTibble(FuentesIliGutData)
sample_table <- getSampleTableFromTibble(meta_tib, rownames="SampleID")
class(sample_table)

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