metaphlan_to_phyloseq: Create a phyloseq object from Metaphlan profiles

In g-antonello/gautils2: Wrapper of my functions to wrangle mostly microbiome data

Create a phyloseq object from Metaphlan profiles

Description

Given the profiles' location, or a pre-loaded table, the function creates a taxonomic table and creates a phyloseq object. if metadata and phylogenetic tree are available, it will try to include those

Usage

metaphlan_to_phyloseq(
  mpa,
  metadata = NULL,
  version = 4,
  verbose = TRUE,
  tax_lvl = "Species"
)

Arguments

mpa	Either a character vector containing the path to the text table to read, or the already-read object
metadata	If in possession, add metadata to the phyloseq object. make sure the name and order of samples is correct for the mpa columns and metadata rows
version	the metaphlan version, by default, version 4 is taken (to date it is the latest - Apr 2022). Versions below 3 are not supported
verbose	logical, whether you want to see which samples did not match between the otu and metadata tables
tax_lvl	character, with the taxonomic level (eg. Phylum, Class, ..., Genus, Species) that you want to have in the phyloseq

Value

A phyloseq object

Examples

data("metaphlanData")

meta_physeq <- metaphlan_to_phyloseq <- function(metaphlanData,
metadata = NULL,
phyloTree = NULL,
version = 4)

g-antonello/gautils2 documentation built on Nov. 28, 2022, 9:39 a.m.