importMetaPhlAn: Import Metaphlan results to 'TreeSummarizedExperiment'

In microbiome/mia: Microbiome analysis

Import Metaphlan results to TreeSummarizedExperiment

Description

Import Metaphlan results to TreeSummarizedExperiment

Arguments

file	a single character value defining the file path of the Metaphlan file. The file must be in merged Metaphlan format.
colData	a DataFrame-like object that includes sample names in rownames, or a single character value defining the file path of the sample metadata file. The file must be in tsv format (default: colData = NULL).
sample_meta	a DataFrame-like object that includes sample names in rownames, or a single character value defining the file path of the sample metadata file. The file must be in tsv format (default: sample_meta = NULL).
phy_tree	a single character value defining the file path of the phylogenetic tree. (default: phy_tree = NULL).
...	additional arguments: assay.type: A single character value for naming assay (default: assay.type = "counts") assay_name: A single character value for specifying which assay to use for calculation. (Please use assay.type instead. At some point assay_name will be disabled.) removeTaxaPrefixes: TRUE or FALSE: Should taxonomic prefixes be removed? (default: removeTaxaPrefixes = FALSE) remove.suffix: TRUE or FALSE: Should suffixes of sample names be removed? Metaphlan pipeline adds suffixes to sample names. Suffixes are formed from file names. By selecting remove.suffix = TRUE, you can remove pattern from end of sample names that is shared by all. (default: remove.suffix = FALSE) set.ranks: TRUE or FALSE: Should the columns in the rowData that are treated as taxonomy ranks be updated according to the ranks found in the imported data? (default: set.ranks = FALSE)

Details

Import Metaphlan (versions 2, 3 and 4 supported) results. Input must be in merged Metaphlan format. (See the Metaphlan documentation and merge_metaphlan_tables method.) Data is imported so that data at the lowest rank is imported as a TreeSummarizedExperiment object. Data at higher rank is imported as a SummarizedExperiment objects which are stored to altExp of TreeSummarizedExperiment object.

Currently Metaphlan versions 2, 3, and 4 are supported.

Value

A TreeSummarizedExperiment object

Author(s)

Leo Lahti and Tuomas Borman. Contact: microbiome.github.io

References

Beghini F, McIver LJ, Blanco-Míguez A, Dubois L, Asnicar F, Maharjan S, Mailyan A, Manghi P, Scholz M, Thomas AM, Valles-Colomer M, Weingart G, Zhang Y, Zolfo M, Huttenhower C, Franzosa EA, & Segata N (2021) Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife. 10:e65088. doi: 10.7554/eLife.65088

See Also

importHUMAnN makeTreeSEFromPhyloseq makeTreeSEFromBiom makeTreeSEFromDADA2 importQIIME2 importMothur

Examples

# (Data is from tutorial
# https://github.com/biobakery/biobakery/wiki/metaphlan3#merge-outputs)

# File path
file_path <- system.file("extdata", "merged_abundance_table.txt", package = "mia")
# Import data
tse <- importMetaPhlAn(file_path)
# Data at the lowest rank
tse
# Data at higher rank is stored in altExp
altExps(tse)
# Higher rank data is in SE format, for example, Phylum rank
altExp(tse, "Phylum")

microbiome/mia documentation built on April 27, 2024, 4:04 a.m.