readMergedMetaphlan: Read Merged Metaphlan Table

In RIVM-IIV-Microbiome/biomeUtils: Utilities for microbiome analytics

Read Merged Metaphlan Table

Description

Read Merged Metaphlan Table

Usage

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.

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.

Value

A phyloseq object

Author(s)

Sudarshan A. Shetty

References

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

Examples

## Not run: 

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)

## End(Not run)

RIVM-IIV-Microbiome/biomeUtils documentation built on July 20, 2023, 10:29 a.m.