Create a GlycoproteomicSE object

GlycoproteomicSE() creates a single-assay SummarizedExperiment::SummarizedExperiment() subclass for glycoproteomics data. It is a thin wrapper around SummarizedExperiment() with additional Glycoverse validation:

1. Exactly one assay is allowed. Extra assays are rejected to avoid ambiguous glycoproteomics measurements.

2. The assay must contain only non-negative values. Raw glycoproteomics abundance data are non-negative; log transformation should be handled by downstream Glycoverse packages.

3. rowData must contain protein, protein_site, and glycan_composition columns. The protein column must be character, protein_site must be integer-like, and glycan_composition must be a glyrepr::glycan_composition() vector. A glycan_structure column is optional, but if present it must be a glyrepr::glycan_structure() vector.

4. metadata must contain a glycan_type field.

This container is experimental and is not recognized by all Glycoverse packages yet. It is intended to become a recommended entry point as package contracts migrate toward SummarizedExperiment-based containers.

Usage

GlycoproteomicSE(abundance, ...)

Arguments

abundance

A numeric abundance matrix with glycopeptides or glycoforms as rows and samples as columns.

...

Arguments passed to SummarizedExperiment::SummarizedExperiment().

• rowData: A S4Vectors::DataFrame() with at least the following columns:

  • protein: required, a character vector

  • protein_site: required, an integer-like vector

  • glycan_composition: required, a glyrepr::glycan_composition() vector

  • glycan_structure: optional, a glyrepr::glycan_structure() vector

• colData: A S4Vectors::DataFrame().

• metadata: A list. It must include a glycan_type field with one of "N", "O", "O-GalNAc", "O-Man", "O-Fuc", "O-GlcNAc", "O-Glc", "HMO", "GSL", "GAG", or "GPI".

Value

A GlycoproteomicSE object.

S4 class

GlycoproteomicSE is an S4 class that extends SummarizedExperiment::SummarizedExperiment().

See also

GlycomicSE()