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Summarize Exposure Variables

Source: R/run_summarize_exposures.R
run_summarize_exposures.Rd

Computes summary statistics for numeric exposure variables and optionally stores the results in the MultiAssayExperiment metadata.

Usage

run_summarize_exposures(expomicset, exposure_cols = NULL, action = "add")

Arguments

expomicset

A MultiAssayExperiment object containing exposure data in the sample metadata.

exposure_cols

A character vector of exposure variable names to summarize. If NULL, all numeric exposure variables are included.

action

A string specifying the action to take. Use "add" to attach the summary table to metadata(expomicset) or "get" to return the summary table directly. Default is "add".

Value

A modified MultiAssayExperiment object (if action = "add"), or a data frame of summary statistics (if action = "get").

Details

This function:

  • Extracts sample-level exposure data using pivot_sample().

  • Filters to user-specified exposures (exposure_cols) if provided.

  • Computes descriptive statistics for each numeric variable:

    • Number of values (n_values)

    • Number of NAs (n_na)

    • Minimum, maximum, and range

    • Sum, median, mean

    • Standard error of the mean

    • 95% confidence interval of the mean

    • Variance, standard deviation

    • Coefficient of variation (sd / mean)

  • Merges the result with variable metadata stored in metadata(expomicset)$codebook.

Examples

if (FALSE) { # \dontrun{
# Add summaries to metadata
expom <- run_summarize_exposures(expom)

# Retrieve just the summary table
summary_df <- run_summarize_exposures(expom, action = "get")
} # }