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Construct an ExploreDataset instance from a path, URL, or SE

Source: R/new_explore_dataset.R
new_explore_dataset.Rd

Factory function: loads the input (or accepts a live SummarizedExperiment), classifies its shape via detect_se_shape(), and returns the appropriate concrete subclass.

Usage

new_explore_dataset(input)

Arguments

input

See above.

Value

An object inheriting from ExploreDataset.

Details

Accepted inputs:

  • A live SummarizedExperiment object.

  • A character path to an .rds / .qs2 file.

  • A character path to a .RData file (Mageck EzResult convention).

  • A character path to a directory containing one of the standard SUSHI artefacts (deResult.rds, rawData_final.rds, etc.).

  • An http(s):// URL pointing at an .rds file.

Examples

# From a live SummarizedExperiment
se <- readRDS(system.file("examples/proteomics/SummarizedExperiment.rds", package = "exploreDE"))
eds <- new_explore_dataset(se)
class(eds)[1]
#> [1] "ExploreDatasetSE_Proteomics"

# From an .h5ad file written by build_explore_h5ad()
path <- build_explore_h5ad(
  SummarizedExperiment::assay(se, "rawData"),
  out = tempfile(fileext = ".h5ad"),
  omics = "proteomics",
  coldata = SummarizedExperiment::colData(se)
)
eds_h5ad <- new_explore_dataset(path)
class(eds_h5ad)[1]
#> [1] "ExploreDatasetH5AD"
eds_h5ad$has_de()
#> [1] FALSE