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Convert SummarizedExperiment to experiment

Source: R/se.R
from_se.Rd

Convert a SummarizedExperiment object to an experiment() object. This function maps the SummarizedExperiment structure to experiment format:

  • The main assay becomes expr_mat

  • colData becomes sample_info

  • rowData becomes var_info

  • metadata becomes meta_data

[Deprecated]

This legacy API is retained temporarily for compatibility. Use GlycomicSE() or GlycoproteomicSE() as the default data container.

Usage

from_se(se, assay_name = NULL, exp_type = NULL, glycan_type = NULL)

Arguments

se

A SummarizedExperiment object to convert.

assay_name

Character string specifying which assay to use. If NULL (default), uses the first assay.

exp_type

Character string specifying experiment type. Must be either "glycomics", "glycoproteomics", "traitomics", "traitproteomics", or "others". If not supplied, will try to extract from metadata. If unavailable there, an error is issued.

glycan_type

Character string specifying glycan type. Must be one of the valid glycan_type values accepted by experiment(). If not supplied, will try to extract from metadata. If unavailable there, an error is issued unless exp_type is "others", where NULL is allowed.

Value

An experiment() object.