Package 'HuMMANet'

HuMMANet: Paired Human Microbiome-Metabolome Study Data

Description

HuMMANet is a Bioconductor experiment data package that provides access to curated paired human microbiome-metabolome studies. The package organizes matched sample metadata, species abundance profiles, original and harmonized metabolite profiles, and study-specific annotation resources including metabolite identifier mappings, microbial producer annotations, disease associations, pathway annotations, and drug similarity matches through Bioconductor ExperimentHub.

Details

Study resources are designed to support reproducible access to paired species and metabolite data across studies through a consistent set of functions. Each study is represented as a MultiAssayExperiment::MultiAssayExperiment with matched sample metadata stored in colData(), assay-level species and metabolite profiles stored in experiments(), and long-form annotation tables attached in metadata(). HuMMANet data can be discovered and retrieved from Bioconductor ExperimentHub using convenience accessors such as HuMMANetHub, HuMMANet_studies, HuMMANet_study_index, HuMMANet_load_modality, and HuMMANet_load_study.

Value

This help page documents the HuMMANet package as a whole and does not return a value.

See Also

HuMMANet, HuMMANetHub, HuMMANet_resource_table, HuMMANet_study_index, HuMMANet_load_modality, HuMMANet_load_study

---

HuMMANet Accessor

Description

Main convenience loader for HuMMANet data.

Usage

HuMMANet(
  studies = NULL,
  modalities = HuMMANet_public_modality_names(),
  extdata_dir = NULL,
  drop_missing = TRUE,
  localHub = FALSE
)

Arguments

studies	Optional character vector of studies to load. Defaults to all.
modalities	Character vector of modalities to load.
extdata_dir	Optional explicit path to a local development 'extdata' directory.
drop_missing	If 'TRUE', missing modalities are omitted from output.
localHub	Logical scalar passed to 'ExperimentHub::ExperimentHub()' when hub access is used.

Value

Named list keyed by study, where each element is a 'MultiAssayExperiment'.

Examples

extdata_dir <- system.file("extdata", package = "HuMMANet")
if (dir.exists(file.path(extdata_dir, "studies"))) {
  out <- HuMMANet(
    studies = "WuY_2025",
    modalities = c("MetadataProfile", "OriginalMetaboliteProfile"),
    extdata_dir = extdata_dir
  )
  names(out)
}

---

List Available Modalities for a Study

Description

List Available Modalities for a Study

Usage

HuMMANet_available_modalities(study, extdata_dir = NULL, localHub = FALSE)

Arguments

study	Study identifier (for example '"FranzosaE_2019"').
extdata_dir	Optional explicit path to a local development 'extdata' directory.
localHub	Logical scalar passed to 'ExperimentHub::ExperimentHub()' when hub access is used.

Value

Character vector of public HuMMANet modality names.

Examples

extdata_dir <- system.file("extdata", package = "HuMMANet")
if (dir.exists(file.path(extdata_dir, "studies"))) {
  HuMMANet_available_modalities("WuY_2025", extdata_dir = extdata_dir)
}

---

Load a Single Modality for One Study

Description

Load a Single Modality for One Study

Usage

HuMMANet_load_modality(
  study,
  modality = HuMMANet_public_modality_names(),
  extdata_dir = NULL,
  allow_missing = FALSE,
  localHub = FALSE
)

Arguments

study	Study identifier.
modality	One public HuMMANet modality name.
extdata_dir	Optional explicit path to a local development 'extdata' directory.
allow_missing	If 'TRUE', return 'NULL' when modality is missing.
localHub	Logical scalar passed to 'ExperimentHub::ExperimentHub()' when hub access is used.

Value

A 'DataFrame', 'SummarizedExperiment', annotation 'data.frame', or 'NULL' if missing and 'allow_missing = TRUE'.

Examples

extdata_dir <- system.file("extdata", package = "HuMMANet")
if (dir.exists(file.path(extdata_dir, "studies"))) {
  md <- HuMMANet_load_modality(
    "WuY_2025",
    "MetadataProfile",
    extdata_dir = extdata_dir
  )
  dim(md)
}

---

Load Curated Data for One Study

Description

Load one study from the HuMMANet 'ExperimentHub' resources. For local development you may pass 'extdata_dir' to read directly from csv files.

Usage

HuMMANet_load_study(
  study,
  modalities = HuMMANet_public_modality_names(),
  extdata_dir = NULL,
  drop_missing = TRUE,
  localHub = FALSE
)

Arguments

study	Study identifier.
modalities	Character vector of modalities to load.
extdata_dir	Optional explicit path to a local development 'extdata' directory.
drop_missing	If 'TRUE', missing modalities are omitted from output.
localHub	Logical scalar passed to 'ExperimentHub::ExperimentHub()' when hub access is used.

Value

A study-level 'MultiAssayExperiment'.

Examples

extdata_dir <- system.file("extdata", package = "HuMMANet")
if (dir.exists(file.path(extdata_dir, "studies"))) {
  x <- HuMMANet_load_study(
    "WuY_2025",
    modalities = c("MetadataProfile", "harmonizedMetaboliteProfile"),
    extdata_dir = extdata_dir
  )
  class(x)
  names(MultiAssayExperiment::experiments(x))
}

---

HuMMANet Resource Table

Description

Inspect the expected HuMMANet ExperimentHub resources.

Usage

HuMMANet_resource_table(localHub = FALSE, extdata_dir = NULL)

Arguments

localHub	Logical scalar passed to 'ExperimentHub::ExperimentHub()'.
extdata_dir	Optional explicit path to a local development 'extdata' directory.

Value

A 'data.frame' describing the HuMMANet records.

Examples

extdata_dir <- system.file("extdata", package = "HuMMANet")
tbl <- HuMMANet_resource_table(extdata_dir = extdata_dir)
head(tbl[, c("title", "record_type")])

---

List Available Studies

Description

List Available Studies

Usage

HuMMANet_studies(extdata_dir = NULL, localHub = FALSE)

Arguments

extdata_dir	Optional explicit path to a local development 'extdata' directory.
localHub	Logical scalar passed to 'ExperimentHub::ExperimentHub()' when hub access is used.

Value

Character vector of study identifiers.

Examples

extdata_dir <- system.file("extdata", package = "HuMMANet")
head(HuMMANet_studies(extdata_dir = extdata_dir))

---

Study Index for HuMMANet

Description

Read the HuMMANet study index. By default this uses the 'ExperimentHub' resource when available and falls back to the packaged 'study_index.csv'.

Usage

HuMMANet_study_index(extdata_dir = NULL, localHub = FALSE)

Arguments

extdata_dir	Optional explicit path to a local development 'extdata' directory.
localHub	Logical scalar passed to 'ExperimentHub::ExperimentHub()' when hub access is used.

Value

A 'data.frame' with one row per study and modality file metadata.

Examples

extdata_dir <- system.file("extdata", package = "HuMMANet")
idx <- HuMMANet_study_index(extdata_dir = extdata_dir)
head(idx[, c("study", "study_slug")])

---

HuMMANet ExperimentHub Records

Description

Return the 'ExperimentHub' subset associated with 'HuMMANet'.

Usage

HuMMANetHub(localHub = FALSE)

Arguments

localHub

Logical scalar passed to 'ExperimentHub::ExperimentHub()'.

Value

An 'ExperimentHub' subset filtered to 'package == "HuMMANet"'.

Examples

if (interactive()) {
  hub <- HuMMANetHub(localHub = TRUE)
  hub
}

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