MetAlyzer_dataset: Open file and read data

In MetAlyzer: Read and Analyze 'MetIDQ™' Software Output Files

Open file and read data

Description

This function creates a SummarizedExperiment (SE) from the given 'MetIDQ' output Excel sheet: metabolites (rowData), meta data (colData), concentration data (assay), quantification status(assay) The column "Sample Type" and the row "Class" are used as anchor cells in the Excel sheet and are therefore a requirement.

Usage

MetAlyzer_dataset(
  file_path,
  sheet = 1,
  status_list = list(Valid = c("#B9DE83", "#00CD66"), LOQ = c("#B2D1DC", "#7FB2C5",
    "#87CEEB"), LOD = c("#A28BA3", "#6A5ACD"), `ISTD Out of Range` = c("#FFF099",
    "#FFFF33"), Invalid = "#FFFFCC", Incomplete = c("#CBD2D7", "#FFCCCC")),
  silent = FALSE
)

Arguments

file_path	A character specifying the file path to the Excel file.
sheet	A numeric index specifying which sheet of the Excel file to use.
status_list	A list of HEX color codes for each quantification status.
silent	If TRUE, mute any print command.

Value

A Summarized Experiment object

Examples

metalyzer_se <- MetAlyzer_dataset(file_path = example_extraction_data())

MetAlyzer documentation built on April 3, 2025, 6:32 p.m.