Pivot a selected omics dataset from a MultiAssayExperiment into tidybulk format

Extracts a specified omics dataset from a MultiAssayExperiment, optionally filters by feature (row) names, and returns a tidy tibble. The output includes assay values along with sample metadata and feature metadata.

Usage

pivot_exp(exposomicset, exp_name, features = NULL)

Arguments

exposomicset: A MultiAssayExperiment object containing one or more omics assays.
exp_name: A character string. The name of the omics dataset to extract (e.g., "Proteomics").
features: Optional character vector of row (feature) names to retain. If NULL, all features are included.

Value

A tibble in tidy format with one row per feature/sample pair, including all metadata and a new column exp_name indicating the assay source. Assay values are provided in separate columns named after the assay slot(s).

Examples

# create example data
mae <- make_example_data(
    n_samples = 10,
    return_mae = TRUE
)
#> Ensuring all omics datasets are matrices with column names.
#> Creating SummarizedExperiment objects.
#> Creating MultiAssayExperiment object.
#> MultiAssayExperiment created successfully.

# pivot experiment
exp_data <- pivot_exp(
    exposomicset = mae,
    exp_name = "mRNA",
    features = c("feat_42")
)