Extract Merged Omics and Exposure Data Frame

This function extracts and merges exposure variables from colData with selected features from omics datasets in a MultiAssayExperiment object. Optionally applies log2 transformation to omics data and restricts features based on a variable map.

Usage

extract_omics_exposure_df(expomicset, variable_map = NULL, log2_trans = TRUE)

Arguments

expomicset

A MultiAssayExperiment object containing omics and exposure data.

variable_map

A data frame with columns "variable" and "exp_name", indicating which variables belong to each omics or exposure domain.

log2_trans

Logical; whether to log2-transform omics data. Default is TRUE.

Value

A data frame where rows correspond to samples, and columns contain exposure variables and log2-transformed omics features. Columns from different omics types are disambiguated using prefixes.

Details

If variable_map is provided, it is used to select variables from both exposures and omics. If not provided, all numeric colData variables are used as exposures (excluding variables matching ^PC), and all omics features are included.

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.
# export the omics exposure df
merged_df <- extract_omics_exposure_df(
    mae,
    log2_trans = TRUE
)
#> Log2-Transforming each assay in MultiAssayExperiment.