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 in the structure of tidybulk::tidybulk(). The output includes assay values along with sample metadata (from colData) and feature metadata (from rowData).

Usage

pivot_exp(expomicset, omics_name, features = NULL)

Arguments

expomicset

A MultiAssayExperiment object containing omics assays.

omics_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 tidybulk format with one row per feature/sample pair, including all metadata and a new column exp_name indicating the assay source.

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 <- mae |>
    pivot_exp(
        omics_name = "mRNA",
        features = "feat_42"
    )