Create an Exposomicset Object

Constructs a MultiAssayExperiment object from exposure data and optionally omics datasets, ensuring proper formatting and alignment of samples and features. For epidemiology-only workflows, omics data can be omitted.

Usage

create_exposomicset(codebook, exposure, omics = NULL, row_data = NULL)

Arguments

codebook

A data frame containing variable information metadata.

exposure

A data frame containing exposure data, with rows as samples and columns as variables.

omics

An optional list of matrices or a single matrix representing omics data. Each matrix should have samples as columns and features as rows. If NULL, creates an exposure-only exposomicset. Default is NULL.

row_data

An optional list of DataFrame objects providing feature metadata for each omics dataset. If NULL, row metadata is generated automatically. Default is NULL.

Value

A MultiAssayExperiment object containing the formatted exposure and optionally omics datasets.

Details

The function validates inputs and creates a MultiAssayExperiment object. If omics data is provided, it converts matrices into SummarizedExperiment objects with proper sample alignment. If omics is NULL, the function creates an exposure-only object suitable for epidemiological analyses using run_association() with source = "exposures".

Examples

# Epi user workflow
# so no omics data
epi_data <- data.frame(
    pm25 = rnorm(10),
    outcome = rbinom(10, 1, 0.5),
    age = rnorm(10, 45, 10),
    row.names = paste0("subj_", 1:10)
)

codebook <- data.frame(
    variable = c("pm25", "outcome", "age"),
    category = c("exposure", "outcome", "covariate")
)

mae <- create_exposomicset(
    codebook = codebook,
    exposure = epi_data
)
#> No omics data provided. Creating exposure-only exposomicset.
#> MultiAssayExperiment created successfully.

# Multi-omics workflow
tmp <- make_example_data(n_samples = 10)

mae <- create_exposomicset(
    codebook = tmp$codebook,
    exposure = tmp$exposure,
    omics = tmp$omics,
    row_data = tmp$row_data
)
#> Ensuring all omics datasets are matrices with column names.
#> Creating SummarizedExperiment objects.
#> Creating MultiAssayExperiment object.
#> MultiAssayExperiment created successfully.