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curatedMetagenomicData R/Bioconductor Package

repository·devel·Indexed 41 days ago

https://github.com/waldronlab/curatedmetagenomicdata

An R/Bioconductor package providing standardized, curated human microbiome data. It offers access to gene families, marker abundances, pathway abundances, and taxonomic profiles (calculated via MetaPhlAn3 and HUMAnN3) delivered as SummarizedExperiment or TreeSummarizedExperiment objects.

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What's inside curatedMetagenomicData

  1. Understand the data structure of curatedMetagenomicData

    devel

    When dryrun = FALSE, the curatedMetagenomicData() function returns a list containing one or more SummarizedExperiment or TreeSummarizedExperiment objects.

    • Single resource requested: Returns a single-element list containing the object.
    • Multiple resources requested: Returns a named list where each element corresponds to a matched resource.

    Data includes standardized metagenomic information such as gene families, marker abundance/presence, pathway abundance/coverage, and relative abundance. Taxonomic abundances are calculated via MetaPhlAn3, and metabolic functional potential via HUMAnN3.

  2. Overview of curatedMetagenomicData

    devel

    The curatedMetagenomicData R package provides standardized, curated human microbiome data for novel analyses. It includes various data types such as gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples from different body sites.

    Key technical details:

    • Taxonomic abundances (bacterial, fungal, and archaeal) are calculated using MetaPhlAn3.
    • Metabolic functional potential is calculated using HUMAnN3.
    • Data Formats: Manually curated sample metadata and standardized metagenomic data are provided as SummarizedExperiment and/or TreeSummarizedExperiment objects.

  3. Install curatedMetagenomicData

    devel

    You can install the package via Bioconductor (recommended) or directly from GitHub.

    From Bioconductor:

    BiocManager::install("curatedMetagenomicData")

    From GitHub:

    BiocManager::install("waldronlab/curatedMetagenomicData", dependencies = TRUE, build_vignettes = TRUE)
    BiocManager::install("curatedMetagenomicData")

  4. Query and retrieve data with curatedMetagenomicData()

    devel

    The curatedMetagenomicData() function is the primary method for querying and retrieving resources.

    Querying Resources

    By default, calling the function with a pattern returns only the titles of the matching resources. Use regular expressions to match resource names.

    Retrieving Data

    To actually download and return the data objects, set dryrun = FALSE. The function returns a list containing SummarizedExperiment or TreeSummarizedExperiment objects.

    Key Arguments

    • dryrun: Set to FALSE to return the actual data objects instead of just titles.
    • rownames: For relative_abundance resources, determines the row identifier type:
      • "long" (default)
      • "short" (species name)
      • "NCBI" (NCBI Taxonomy ID)
    • counts: When set to TRUE, relative abundance proportions are multiplied by read depth and rounded to the nearest integer before being returned.

    When multiple resources are requested, the returned list will contain named elements corresponding to each object.

    # Querying titles only
curatedMetagenomicData("AsnicarF_20.+")

# Retrieving a single resource with specific rownames
curatedMetagenomicData("AsnicarF_2017.relative_abundance", dryrun = FALSE, rownames = "short")

# Retrieving multiple resources as integer counts
curatedMetagenomicData("AsnicarF_20.+.relative_abundance", dryrun = FALSE, counts = TRUE, rownames = "short")