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Convert experiment to SummarizedExperiment

as_se.Rd

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

  • expr_mat becomes the main assay

  • sample_info becomes colData

  • var_info becomes rowData

  • meta_data becomes metadata

Usage

as_se(exp, assay_name = "counts")

Arguments

exp

An experiment() object to convert.

assay_name

Character string specifying the name for the assay. Default is "counts".

Value

A SummarizedExperiment object.

Examples

# Convert toy experiment to SummarizedExperiment
se <- as_se(toy_experiment)
#> Warning: replacing previous import ‘S4Arrays::makeNindexFromArrayViewport’ by ‘DelayedArray::makeNindexFromArrayViewport’ when loading ‘SummarizedExperiment’
se
#> class: SummarizedExperiment 
#> dim: 4 6 
#> metadata(2): exp_type glycan_type
#> assays(1): counts
#> rownames(4): V1 V2 V3 V4
#> rowData names(3): protein peptide glycan_composition
#> colnames(6): S1 S2 ... S5 S6
#> colData names(2): group batch