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Identification overview

count_compositions.Rd

These functions are used to identify the number of glycan compositions, glycan structures, glycopeptides, peptides, glycoforms, glycoproteins, and glycosites in an experiment().

Usage

count_compositions(x)

count_structures(x)

count_peptides(x)

count_glycopeptides(x, count_struct = NULL)

count_glycoforms(x, count_struct = NULL)

count_proteins(x)

count_glycosites(x)

Arguments

x

An experiment() object.

count_struct

For count_glycopeptides() and count_glycoforms(), whether to count the number of glycan structures or glycopeptides. If TRUE, glycopeptides or glycoforms bearing different glycan structures with the same glycan composition are counted as different ones. If not provided (NULL), defaults to TRUE if glycan_structure column exists in the variable information tibble, otherwise FALSE.

Value

An integer.

  • count_compositions(): The number of glycan compositions.

  • count_structures(): The number of glycan structures.

  • count_peptides(): The number of peptides.

  • count_glycopeptides(): The number of unique combinations of peptides, sites, and glycans.

  • count_glycoforms(): The number of unique combinations of proteins, sites, and glycans.

  • count_proteins(): The number of proteins.

  • count_glycosites(): The number of unique combinations of proteins and sites.

Details

The following columns are required in the variable information tibble:

  • count_compositions(): glycan_composition

  • count_structures(): glycan_structure

  • count_peptides(): peptide

  • count_glycopeptides(): glycan_composition or glycan_structure, peptide, peptide_site

  • count_glycoforms(): glycan_composition or glycan_structure, protein or proteins, protein_site or protein_sites

  • count_proteins(): protein or proteins

  • count_glycosites(): protein or proteins, protein_site or protein_sites

You can use count_struct parameter to control how to count glycopeptides and glycoforms, either by glycan structures or by glycan compositions.