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Convert SummarizedExperiment to experiment

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

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" or "glycoproteomics". If NULL, will try to extract from metadata, otherwise defaults to "glycomics".

glycan_type

Character string specifying glycan type. Must be either "N" or "O". If NULL, will try to extract from metadata, otherwise defaults to "N".

Value

An experiment() object.

Examples

# Convert SummarizedExperiment back to experiment
se <- as_se(toy_experiment)
exp_back <- from_se(se, exp_type = "glycomics", glycan_type = "N")
exp_back
#> 
#> ── Glycomics Experiment ────────────────────────────────────────────────────────
#> ℹ Expression matrix: 6 samples, 4 variables
#> ℹ Sample information fields: group <chr>, batch <dbl>
#> ℹ Variable information fields: protein <chr>, peptide <chr>, glycan_composition <chr>