Convert SummarizedExperiment to tibble

Source: R/tibble_methods.R

Converts a SummarizedExperiment object to a tibble format, combining assay data with sample and feature metadata in a long format suitable for tidyverse workflows.

# S3 method for class 'SummarizedExperiment'
as_tibble(
  x,
  ...,
  .name_repair = c("check_unique", "unique", "universal", "minimal"),
  rownames = pkgconfig::get_config("tibble::rownames", NULL)
)

Arguments

x

A SummarizedExperiment object to convert.

...

Additional arguments passed to internal conversion functions.

.name_repair

Treatment of problematic column names. See as_tibble for details.

rownames

Either NULL or a string giving the name of a column to use as rownames. See as_tibble for details.

Value

A tibble containing the assay data combined with sample and feature metadata. The structure includes:

  • Feature identifiers (from rownames or rowData)

  • Sample identifiers (from colnames or colData)

  • Assay values (one column per assay)

  • Sample metadata (from colData)

  • Feature metadata (from rowData)

Details

This method provides a bridge between Bioconductor's SummarizedExperiment objects and tidyverse data manipulation workflows. The conversion creates a long-format tibble where each row represents a feature-sample combination, making it suitable for filtering, grouping, and other tidyverse operations.

Examples

if (FALSE) { # \dontrun{
  library(tidyprint)
  data(se_airway)
  as_tibble(se_airway)
} # }