Aggregate Data

Aggregate glycoproteomics data to different levels (glycoforms, glycopeptides, etc.). This function sums up quantitative values for each unique combination of specified variables. It is recommended to call this function after missing value imputation.

The following levels are available:

• "gf": Aggregate to glycoforms, which is the unique combination of proteins, protein sites, and glycan compositions. This is the default level.

• "gp": Aggregate to glycopeptides, which is the unique combination of peptides, proteins, protein sites, and glycan compositions.

• "gfs": Like "gf", but differentiates structures with the same composition.

• "gps": Like "gp", but differentiates structures with the same composition.

Different levels of aggregation require different columns in the variable information.

• "gf": "protein", "gene", "glycan_composition", "protein_site"

• "gp": "peptide", "protein", "gene", "glycan_composition", "peptide_site", "protein_site"

• "gfs": "protein", "gene", "glycan_composition", "glycan_structure", "protein_site"

• "gps": "peptide", "protein", "gene", "glycan_composition", "glycan_structure", "peptide_site", "protein_site"

Note that aggregate() will remove all other columns in the variable information except the ones listed above. So please call aggregate() as early as possible, before calling add_site_seq() or other motif annotation functions in glymotif.

Usage

aggregate(exp, to_level = c("gf", "gp", "gfs", "gps"))

Arguments

exp

A glyexp_experiment object containing glycoproteomics data. This function only works with glyexp_experiment objects as it requires variable information for aggregation.

to_level

The aggregation level, one of: "gf" (glycoforms), "gp" (glycopeptides), "gfs" (glycoforms with structures), or "gps" (glycopeptides with structures). See Details for more information.

Value

A modified glyexp_experiment object with aggregated expression matrix and updated variable information.