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Write Data Processing Report (EXCEL)

Source: R/data-export.R
save_report_xlsx.Rd

Generates a data processing report from a MidarExperiment object and writes it to an Excel file. The report includes information on the data processing steps, quality control metrics, feature concentrations, and metadata. Following tables will be created as sheets in the EXCEL file:

Usage

save_report_xlsx(data = NULL, path, filtered_variable = "conc")

Arguments

data

A MidarExperiment object containing original and processed data and metadata.

path

A character string specifying the file name and path for the Excel file. If the path does not include an .xlsx extension, it is added automatically.

filtered_variable

A character string specifying the variable name in the filtered data to be exported. It must be one of "conc", "intensity", "norm_intensity", "response", "area", "height", "conc_raw", "rt", or "fwhm". The defined variable name will be included in the sheet name. Default is "conc".

Value

The function does not return a value. It writes the report to the specified Excel file.

Details

  • Info: General information including date, author, and MiDAR version, processing status and feature concentration unit.

  • Feature_QC_metrics: Quality control metrics of all features.

  • QCfilt_x_StudySamples: Feature (QC)-filtered data (variable defiend via filtered_variable) in study samples ('SPL'). Filter have to be set via filter_features_qc(). The x corresponds to the filtered_variable argument.

  • QCfilt_x_AllSamples: Feature (QC)-filtered data (variable defiend via filtered_variable) in all samples. Filter have to be set via filter_features_qc(). The x corresponds to the filtered_variable argument.

  • Conc_FullDataset: Final feature concentrations from the full, non-filtered dataset.

  • Raw_Intensity_FullDataset: Raw feature intensities from the full, non-filtered dataset.

  • Norm_Intensity_FullDataset: Normalized feature intensities from the full, non-filtered dataset.

  • SampleMetadata: Analysis metadata that was imported and used for processing steps

  • FeatureMetadata: Feature metadata that was imported and used for processing steps

  • InternalStandards: Internal standards metadata with concentrations

  • BatchInfo: Information on batches and positions of first and last analysis/sample in each batch

#' If certain data sets are not available, the function includes empty tables for the corresponding dataset.

Concentration corresponds to the final concentration values after applying isotope correction, and drift and batch correction, if applicable. If any corrections, such as drift or batch correction, were applied to raw or normalized intensities, the exported values will reflect these corrections.

Examples

if (FALSE) { # \dontrun{
# Assuming `midarexp` is a MidarExperiment object and `output_path` is a valid path
save_report_xlsx(data = midarexp, path = "output_path/report.xlsx")
} # }