Runs all delayed operations on the object

Runs all delayed operations on the object

realize(object, keep_intermediate = NA)

Arguments

object

A GCIMSDataset object, modified in-place

keep_intermediate

A logical, whether to keep the intermediate files of the previous realization once this one finishes. If NA, keeping will depend on the object.

Value

The same GCIMSDataset object, without pending operations

Examples

base_dir <- system.file("extdata", "sample_formats", package = "GCIMS")
annot <- data.frame(SampleID = "Sample1", FileName = "small.mea.gz")
dataset <- GCIMSDataset$new(annot, base_dir)
print(dataset)
#> A GCIMSDataset:
#> - With 1 samples
#> - Stored on disk (not loaded yet)
#> - No phenotypes
#> - No previous history
#> - Queued operations:
#>   - read_sample:
#>       base_dir: /__w/_temp/Library/GCIMS/extdata/sample_formats
#>       parser: default
#>   - setSampleNamesAsDescription
realize(dataset)
#> Warning: realize(object) is deprecated, use object$realize() instead
#> This warning is displayed once per session.
print(dataset)
#> A GCIMSDataset:
#> - With 1 samples
#> - Stored on disk (at /tmp/RtmpEOas8t/GCIMSDataset_tempdir_2c76165835e8/setSampleNamesAsDescription_73f1f13c6c84dc08e93787b4ef62110f)
#> - No phenotypes
#> - History:
#>   - read_sample:
#>       base_dir: /__w/_temp/Library/GCIMS/extdata/sample_formats
#>       parser: default
#>   - setSampleNamesAsDescription
#> - No operations enqueued