Collect Dataset submission metadata interactively

This helper gathers the dataset-level fields needed for the Dataset table. It reuses Trio metadata when already available and only prompts for the remaining values in interactive sessions.

Usage

collectDatasetSubmissionInfo(trio, defaults = list())

Arguments

trio

A Trio object.

defaults

Optional named list of pre-filled values. Any non-NULL value here bypasses the interactive prompt for that field.

Value

A named list ready to pass as dataset_args to buildDatasetSubmission().

Examples

data <- data.frame(feature = c(1, 2, 3), row.names = paste0("sample", 1:3))
labels <- factor(c("A", "B", "A"))
names(labels) <- rownames(data)
trio <- Trio$new(
  data = data,
  evidence = list(class_labels = list(
    evidence = labels,
    metrics = "macroF1Metric"
  )),
  metrics = list(macroF1Metric = macroF1Metric),
  name = "example_dataset",
  description = "A small example dataset."
)
collectDatasetSubmissionInfo(
  trio,
  defaults = list(
    dataType = "omics",
    dataModality = "transcriptomics",
    technology = "RNA-seq",
    tissue = "blood",
    status = "healthy"
  )
)
#> $name
#> [1] "example_dataset"
#> 
#> $dataType
#> [1] "omics"
#> 
#> $dataModality
#> [1] "transcriptomics"
#> 
#> $technology
#> [1] "RNA-seq"
#> 
#> $description
#> [1] "A small example dataset."
#> 
#> $doi
#> [1] NA
#> 
#> $organism
#> [1] NA
#> 
#> $tissue
#> [1] "blood"
#> 
#> $status
#> [1] "healthy"
#>