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Standardize variable IDs in an experiment

Source: R/standardize-variable.R
standardize_variable.Rd

Converts meaningless variable IDs (like "GP1", "V1") into meaningful, human-readable IDs based on the experiment type and available columns.

The format of the new IDs depends on the exp_type if format is not specified:

  • glycomics: {glycan_composition}, e.g., "Hex(5)HexNAc(2)"

  • glycoproteomics: {protein}-<site>-{glycan_composition} or {protein}-{glycan_composition} if no protein_site column exists

  • traitomics: {motif} or {trait} depending on which column is present

  • traitproteomics: {protein}-<site>-{motif} or {protein}-<site>-{trait}

If duplicate IDs are generated (e.g., same composition with multiple PSMs), a unique integer suffix is appended using the unique_suffix pattern.

Usage

standardize_variable(
  exp,
  format = NULL,
  unique_suffix = "-{N}",
  fasta = NULL,
  taxid = 9606
)

Arguments

exp

An experiment().

format

A format string specifying how to construct variable IDs. Use {column_name} to insert values from var_info columns. For example, "{gene}-{glycan_composition}" would produce "GENE1-Hex(5)". If NULL (default), a sensible format is chosen based on exp_type. Use <site> to include the amino acid and position (e.g., "N32"). The <site> token is a special placeholder that gets replaced with <aa><pos> format (e.g., "N32", "S44"). It requires the protein_site column and uses the following decision tree to determine the amino acid:

  1. If peptide and peptide_site columns exist, extract from peptide

  2. Else if fasta is provided, extract from FASTA sequences

  3. Else fetch from UniProt using UniProt.ws

unique_suffix

A string pattern for making IDs unique when duplicates exist. Must contain {N} which will be replaced with the numeric suffix (1, 2, 3...). Default is "-{N}" which produces IDs like "Hex(5)-1", "Hex(5)-2".

fasta

Either a file path to a FASTA file or a named character vector with protein IDs as names and sequences as values. Used to look up amino acids for site representation when peptide columns are not available. Default: NULL (use UniProt.ws to fetch sequences).

taxid

NCBI taxonomy ID for UniProt lookup. Default: 9606 (human).

Value

The experiment with standardized variable IDs, invisibly.

Examples