importMetaPhlAn: Import Metaphlan results to 'TreeSummarizedExperiment'
In microbiome/mia: Microbiome analysis

importMetaPhlAn

R Documentation

Import Metaphlan results to `TreeSummarizedExperiment`

Description

Import Metaphlan results to TreeSummarizedExperiment

Arguments

`file`	`NULL` or `DataFrame`-like object. Defines the file path of the Metaphlan file. The file must be in merged Metaphlan format.
`col.data`	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: `NULL`).
`colData`	Deprecated. use `col.data` instead.
`sample_meta`	Deprecated. Use `col.data` instead.
`tree.file`	`Character scalar`. Defines the file path of the phylogenetic tree. (Default: `NULL`).
`phy_tree`	Deprecated. Use `tree.file` instead.
`...`	additional arguments: `assay.type`: `Character scalar`. Specifies the name of the assay used in calculation. (Default: `"counts"`) `prefix.rm`: `Logical scalar`. Should taxonomic prefixes be removed? (Default: `FALSE`) `remove.suffix`: `Logical scalar`. 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: `FALSE`) `set.ranks`: `Logical scalar`. Should the columns in the rowData that are treated as taxonomy ranks be updated according to the ranks found in the imported data? (Default: `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

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

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 Nov. 20, 2024, 1:12 a.m.