Get tibble

Get tibble

getAbundanceTibble(
  x,
  column_id = "FeatureID",
  select_rows = NULL,
  select_cols = NULL
)

getTaxaTibble(
  x,
  column_id = "FeatureID",
  select_rows = NULL,
  select_cols = NULL
)

getSampleTibble(
  x,
  column_id = "SampleID",
  select_rows = NULL,
  select_cols = NULL
)

Arguments

x

phyloseq object

column_id

A character

select_rows

Rows to return in output.

select_cols

Columns to return in output

Value

A tibble

Details

Convert different phyloseq slots into tibbles.

getAbundanceTibble gets the otu_table in tibble format.

getTaxaTibble gets the taxa_table in tibble format.

getSampleTibble gets the sample_data in tibble format.

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)
tax_tib <- getTaxaTibble(FuentesIliGutData)
meta_tib <- getSampleTibble(FuentesIliGutData)