Automatic Aggregation

auto_aggregate() was deprecated in glyclean 0.16.0. Use aggregate() instead; it now selects the aggregation level from the input type and whether glycan_structure is present.

Usage

auto_aggregate(exp, standardize_variable = TRUE)

Arguments

exp

A glycomics or glycoproteomics container: a glyexp::GlycomicSE(), glyexp::GlycoproteomicSE(), or legacy glyexp_experiment object.

standardize_variable

Whether to call glyexp::standardize_variable() after aggregation. Set to FALSE to skip network calls for faster testing. Default is TRUE.

Value

A modified container with the same class as exp, an aggregated expression matrix, and updated variable information.

Examples

library(glyexp)
exp <- real_experiment
# Deprecated:
# auto_aggregate(exp)

# Use instead:
aggregate(exp)
#> 
#> ── GlycoproteomicSE ────────────────────────────────────────────────────────────
#> ℹ Abundance assay: 12 samples, 4001 variables
#> ℹ Glycan type: N
#> ℹ Row data fields: protein <chr>, glycan_composition <comp>, glycan_structure <struct>, protein_site <int>, gene <chr>
#> ℹ Column data fields: group <fct>
#> ℹ Metadata fields: exp_type <chr>, glycan_type <chr>, quant_method <chr>