Standardize variable IDs in an experiment

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}-{protein_site}-{glycan_composition}

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

• traitproteomics: {protein}-{protein_site}-{motif} or {protein}-{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}")

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.

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".

Value

The experiment with standardized variable IDs.

Examples

# Glycomics example
expr_mat <- matrix(1:4, nrow = 2)
rownames(expr_mat) <- c("V1", "V2")
colnames(expr_mat) <- c("S1", "S2")
sample_info <- tibble::tibble(sample = c("S1", "S2"))
var_info <- tibble::tibble(
  variable = c("V1", "V2"),
  glycan_composition = glyrepr::glycan_composition(c(Hex = 5, HexNAc = 2))
)
exp <- experiment(expr_mat, sample_info, var_info,
  exp_type = "glycomics", glycan_type = "N"
)
standardize_variable(exp)
#> 
#> ── Glycomics Experiment ────────────────────────────────────────────────────────
#> ℹ Expression matrix: 2 samples, 2 variables
#> ℹ Sample information fields: none
#> ℹ Variable information fields: glycan_composition <comp>

# Glycoproteomics example
expr_mat <- matrix(1:4, nrow = 2)
rownames(expr_mat) <- c("GP1", "GP2")
colnames(expr_mat) <- c("S1", "S2")
sample_info <- tibble::tibble(sample = c("S1", "S2"))
var_info <- tibble::tibble(
  variable = c("GP1", "GP2"),
  protein = c("P12345", "P12345"),
  protein_site = c(32L, 45L),
  glycan_composition = glyrepr::glycan_composition(c(Hex = 5, HexNAc = 2))
)
exp <- experiment(expr_mat, sample_info, var_info,
  exp_type = "glycoproteomics", glycan_type = "N"
)
standardize_variable(exp)
#> 
#> ── Glycoproteomics Experiment ──────────────────────────────────────────────────
#> ℹ Expression matrix: 2 samples, 2 variables
#> ℹ Sample information fields: none
#> ℹ Variable information fields: protein <chr>, protein_site <int>, glycan_composition <comp>

# Custom format example
standardize_variable(exp, format = "{protein}-{glycan_composition}")
#> 
#> ── Glycoproteomics Experiment ──────────────────────────────────────────────────
#> ℹ Expression matrix: 2 samples, 2 variables
#> ℹ Sample information fields: none
#> ℹ Variable information fields: protein <chr>, protein_site <int>, glycan_composition <comp>