TibbleUtilites: Utilities For 'phyloseq-class' Slots to Tibbles

In microbiome/microbiome: Microbiome Analytics

Utilities For phyloseq-class Slots to Tibbles

Description

Utility to convert phyloseq slots to tibbles.

Usage

otu_tibble(x, column.id = "FeatureID")

tax_tibble(x, column.id = "FeatureID")

sample_tibble(x, column.id = "SampleID")

combine_otu_tax(x, column.id = "FeatureID")

Arguments

x	phyloseq-class object.
column.id	Provide name for the column which will hold the rownames. of slot.

Details

Convert different phyloseq slots into tibbles. otu_tibble gets the otu_table in tibble format. tax_tibble gets the taxa_table in tibble format. combine_otu_tax combines otu_table and taxa_table into one tibble.

Value

A tibble

Author(s)

Contact: Sudarshan A. Shetty [e-mail]

Examples

library(microbiome)
data("dietswap")
otu_tib <- otu_tibble(dietswap,column.id="FeatureID")
tax_tib <- tax_tibble(dietswap,column.id="FeatureID")
sample_tib <- sample_tibble(dietswap,column.id="SampleID")
otu_tax <- combine_otu_tax(dietswap,column.id = "FeatureID")
head(otu_tax)

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.