Read Merged Metaphlan Table

readMergedMetaphlan(
  input_file_path = NULL,
  find_sample_name_pattern = NULL,
  replace_sample_name_pattern = "",
  return_species = TRUE
)

Arguments

input_file_path: path to where the output of Metaphlan3 is located.
find_sample_name_pattern: Naming convention used for samples within the input file.
replace_sample_name_pattern: specific pattern to replace in sample names.
return_species: Logical whether to return only species level data. Default TRUE.

Value

A phyloseq object

Details

This function reads Metaphlan3 output that is merged with all samples. and returns a phyloseq object with otu_table and tax_table.

Note: readMergedMetaphlan is tested for Metaphlan version 3 and based on the RIVM HPC HUMANN3 pipeline output built by Jeron Frank.

References

Shetty SA (2020). Utilities for microbiome analytics. https://github.com/RIVM-IIV-Microbiome/biomeUtils

Author

Sudarshan A. Shetty

Examples

if (FALSE) {

library(biomeUtils)

mpa.ps <- readMergedMetaphlan(input_file_path = "../metaphlan_bugs_list_merged.txt",
                             find_sample_name_pattern = "_kneaddata_concat_metaphlan_bugs_list",
                             replace_sample_name_pattern = "",
                             return_species = TRUE)
}