Get Phyloseq slots from Tibbles

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

Value

Either otu_table or

tax_table or

sample_data

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.

References

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

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
data("FuentesIliGutData")
otu_tib  <- getAbundanceTibble(FuentesIliGutData)
otu_table <- getOtuTableFromTibble(otu_tib, rownames="FeatureID")
class(otu_table)
#> [1] "otu_table"
#> attr(,"package")
#> [1] "phyloseq"

tax_tib <- getTaxaTibble(FuentesIliGutData)
taxa_table <- getTaxaTableFromTibble(tax_tib, rownames="FeatureID")
class(tax_table)
#> [1] "standardGeneric"
#> attr(,"package")
#> [1] "methods"

meta_tib <- getSampleTibble(FuentesIliGutData)
sample_table <- getSampleTableFromTibble(meta_tib, rownames="SampleID")
class(sample_table)
#> [1] "sample_data"
#> attr(,"package")
#> [1] "phyloseq"