getTibble: Get tibble

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

Get tibble

Description

Get tibble

Usage

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

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.

Value

A tibble

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

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