Parse basic MetaPhlAn output for a single sample as a TreeSummarizedExperiment object

'parse_metaphlan_list' reads a file obtained from running MetaPhlAn for microbial profiling (with or without unclassified fraction estimation) or viral sequence cluster analysis. This file is parsed into a TreeSummarizedExperiment object.

Usage

parse_metaphlan_list(sample_id, file_path, data_type)

Arguments

sample_id

String: A sample identifier

file_path

String: Path to a locally stored MetaPhlAn output file in TSV format

data_type

String: The type of MetaPhlAn output file to be parsed, either 'relative_abundance' or 'viral_clusters'

Value

A TreeSummarizedExperiment object with process metadata, row data, column names, and relevant assays.

Details

This function does not integrate sample metadata as column data. The provided sample_id is used as the column name for assays within the TreeSummarizedExperiment object and is intended to be used for integration of sample metadata.

See also

read_delim DataFrame-class, S4VectorsOverview TreeSummarizedExperiment-class, TreeSummarizedExperiment

Examples

if (FALSE) { # \dontrun{
if(interactive()){
 fpath <- file.path(system.file("extdata",
                                package = "parkinsonsMetagenomicData"),
                    "sample_metaphlan_bugs_list.tsv.gz")
 parse_metaphlan_list(sample_id = "004c5d07-ec87-40fe-9a72-6b23d6ec584e",
                      file_path = fpath,
                      data_type = "relative_abundance")
 }
} # }