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Export tidyexposomics Results to Excel

Source: R/extract_results_excel.R
extract_results_excel.Rd

Exports selected results stored in a MultiAssayExperiment object created by the tidyexposomics pipeline to an Excel workbook. Users can select which result types to include, and optionally add placeholder sheets for missing data.

Usage

extract_results_excel(
  expomicset,
  file = "tidyexposomics_results.xlsx",
  result_types = c("correlation", "association", "differential_analysis",
    "multiomics_integration", "network", "enrichment", "exposure_summary", "pipeline"),
  include_empty_tabs = FALSE
)

Arguments

expomicset

A MultiAssayExperiment object with results stored in @metadata, typically created by the tidyexposomics pipeline.

file

Character. Path to the output Excel file.

result_types

Character vector specifying which result categories to export. Options include:

  • "correlation": Correlation results.

  • "association": Association results.

  • "differential_analysis": Differential abundance results, including sensitivity analysis if available.

  • "multiomics_integration": Common top features contributing to latent factors from multi-omics integration.

  • "network": Exposure impact metrics from network analyses.

  • "enrichment": Enrichment results by omic and exposure category.

  • "exposure_summary": Summary statistics for exposure variables.

  • "pipeline": Overview of steps completed in the pipeline.

Use "all" to export all of the above categories.

include_empty_tabs

Logical. If TRUE, adds placeholder sheets for any missing result types. Default is FALSE.

Value

An Excel file is written to the specified path. A message is printed with the file location.

Examples

# Create example data
mae <- make_example_data(
    n_samples = 20,
    return_mae = TRUE
)
#> Ensuring all omics datasets are matrices with column names.
#> Creating SummarizedExperiment objects.
#> Creating MultiAssayExperiment object.
#> MultiAssayExperiment created successfully.

# run correlation analysis
mae <- mae |>
    run_correlation(
        feature_type = "exposures",
        exposure_cols = c("exposure_pm25", "exposure_no2", "age", "bmi")
    )

# file path of the output file
tmp <- tempfile(fileext = ".xlsx")

# extract the correlation results
extract_results_excel(
    expomicset = mae,
    result_types = "correlation",
    file = tmp
)
#> Writing Correlation Results.
#> Results written to: C:\Users\Jason\AppData\Local\Temp\RtmpiGC2jV\file71781e8e34e.xlsx