tibble-constructors: Construct phyloseq objects from tibbles

In mikemc/speedyseq: Faster implementations of phyloseq functions

Construct phyloseq objects from tibbles

Description

These methods extend phyloseq's constructor functions to construct phyloseq components from tibbles (objects with class "tbl_df").

Usage

## S4 method for signature 'tbl_df'
otu_table(object, taxa_are_rows)

## S4 method for signature 'tbl_df'
sample_data(object)

## S4 method for signature 'tbl_df'
tax_table(object)

Arguments

object	A tibble whose first column contains the sample or taxa ids
taxa_are_rows	Logical; TRUE if rows correspond to taxa and FALSE if rows correspond to samples

Details

Since tibbles cannot have row names, the sample or taxon identifiers must be contained in a regular column. Speedyseq currently always uses the first column for the identifiers that would normally be taken from the row names by phyloseq's built-in constructors. Thus the first column is assumed to contain the sample names for sample_data() and the OTU/taxa names for tax_table(); for otu_table(), the first column is assumed to contain the sample names if taxa_are_rows = TRUE and the taxa names if taxa_are_rows = FALSE, with the other identifier being taken from the remaining column names.

See Also

tibble::tbl_df phyloseq::otu_table() phyloseq::sample_data() phyloseq::tax_table()

Examples

## Not run: 
# Read a .csv file with readr, which creates an object of class `tbl_df`
tbl <- readr::read_csv("path/to/otu_table.csv")
# Inspect and check if taxa are rows and that the first column contains the
# sample names or the taxa/OTU names
head(tbl) 
# Create a phyloseq `otu_table` object
otu <- otu_table(tbl, taxa_are_rows = FALSE)

# Read a .csv file with readr, which creates an object of class `tbl_df`
tbl <- readr::read_csv("path/to/sample_data.csv")
# Inspect and check that the first column contains the sample names
head(tbl) 
# Create a phyloseq `sample_data` object
sam <- sample_data(tbl)

## End(Not run)

mikemc/speedyseq documentation built on April 22, 2024, 6:40 p.m.