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Generate Input Table for Proteomic and Phosphoproteomic Analysis

Source: R/dataImport.R
generateInputTable.Rd

generateInputTable generates an input table for proteomic and phosphoproteomic analysis by reading files from a specified folder.

Usage

generateInputTable(rawFolder, batchAsFolder = FALSE)

Arguments

rawFolder

A character string specifying the path to the folder containing the raw files.

batchAsFolder

A logical value indicating whether to treat subdirectories as separate batches. Default is FALSE.

Value

A data.frame with columns fileName, sample, searchType, batch, and id that can be used as input for further analysis.

Details

The function performs the following steps:

  • Optionally treats subdirectories as separate batches.

  • Reads the summary file containing experimental information.

  • Generates unique experimental IDs based on batch and sample names.

  • Processes file paths for full proteome and phosphoproteome data.

  • Creates a combined input table with file names, sample names, search types, batches, and IDs.