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Convert MetaPhlAn profile to phyloseq object

Source: R/metaphlan_to_phyloseq.R
metaphlan_to_phyloseq.Rd

This function converts a MetaPhlAn profile to a phyloseq object when given the file path or a pre-loaded table.

Usage

metaphlan_to_phyloseq(
  mtphlan_profile,
  taxa_lvl = NULL,
  metadata = NULL,
  sample_column = NULL,
  use_taxa_names = FALSE,
  merged_profiles = TRUE
)

Arguments

mtphlan_profile

The MetaPhlAn profile to be converted. It can be either a file path or a data frame of MetaPhlAn profile(s).

taxa_lvl

Optional taxonomic level to filter the profile to. Valid options are 'kingdom', 'phylum', 'class', 'order', 'family', 'genus', 'species' or 't' (SGB). First letter abbreviations are also accepted.

metadata

Optional metadata for the samples. If provided, it should be a data frame.

sample_column

Character string. The column in the metadata containing the sample names. Should match column names of the MetaPhlAn profile.

use_taxa_names

Logical indicating whether to use taxonomic names instead of OTUs in the resulting phyloseq object. Default is FALSE.

merged_profiles

Logical; if TRUE (the default) the file to be loaded is assumed to be multiple merged MetaPhlAn profiles.

Value

A phyloseq object representing the MetaPhlAn profile.

Note

If mtphlan_profile is an already loaded object, the clade names should not be shortened, otherwise the taxonomic table cannot be created. Should you wish to use the taxonomic names of the specified rank as the row names in the phyloseq object, set use_taxa_names = TRUE.

Author

Jérémy Rotzetter

Examples

metaphlan_to_phyloseq(species_only, taxa_lvl = "s")
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 12 taxa and 6 samples ]
#> tax_table()   Taxonomy Table:    [ 12 taxa by 7 taxonomic ranks ]