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Audit raw data headers against tidyproteomics platform configuration

Source: R/input_audit.R
input_audit.Rd

Inspects the column headers of a raw proteomics data file, matches them against the regex patterns defined in the platform configuration, and produces a comprehensive audit table with rules-based recommendations for unmapped or alternative columns (e.g. gene names, descriptions, MaxLFQ intensity).

Usage

input_audit(
  file_name = NULL,
  platform = NULL,
  analyte = c("proteins", "peptides"),
  config = NULL
)

Arguments

file_name

Path to the raw data file (txt, tsv, csv, etc.)

platform

The source of the data (e.g., 'MaxQuant', 'ProteomeDiscoverer', 'FragPipe', 'DIA-NN')

analyte

The omics analyte ('proteins', 'peptides')

config

Optional path to a specific config TSV file, or a data.frame of config rows

Value

A tibble with raw headers, matching status, config mapping, and suggestions

Examples

library(tidyproteomics)
if (FALSE) {
audit <- input_audit("proteinGroups.txt", platform = "MaxQuant", analyte = "proteins")
print(audit)
}