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Read Metadata from a File

Source: R/read_metadata.R
read_metadata.Rd

This function reads metadata from a specified file, validates the file format, and extracts columns that match a predefined set of column names.

Usage

read_metadata(
  file_path,
  header = TRUE,
  sep = ",",
  string_as_factors = FALSE,
  predefined_columns = c("Plate_ID", "Well_ID", "Row", "Column", "Species",
    "Treatment_1", "Concentration_1", "Sample_type", "Barcode")
)

Arguments

file_path

A character string specifying the path to the metadata file. The file must be in CSV or Excel format.

header

Logical. If TRUE, the first row of the file is used as column names. Defaults to TRUE.

sep

A character string specifying the column separator for CSV files. Defaults to ",".

string_as_factors

Logical. If TRUE, character columns in the data frame are converted to factors. Defaults to FALSE.

predefined_columns

A character vector of column names to match in the file. Defaults to a predefined set of column names: c("Plate_ID", "Well_ID", "Row", "Column", "Species", "Cell_type", "Model_type", "Time", "Unit", "Treatment_1", "Concentration_1", "Unit_1", "Sample_type", "Barcode", "Project").

Value

A data frame containing only the matched columns if at least one predefined column is found. Returns NULL and prints an error message if no predefined columns are found.

Details

The function first checks if the file exists and validates its format (CSV or Excel). It then attempts to read the file and match its column names to a predefined set of column names. Supported file formats include:

  • CSV files with .csv extension.

  • Excel files with .xls or .xlsx extensions (requires the readxl package).

Examples

# Example CSV file
file_path <- system.file("/extdata/PMMSq033_metadata.csv", package = "macpie")
result <- read_metadata(file_path)