Build DatasetEvidence submission rows from a Trio object

This helper creates one DatasetEvidence row per supporting evidence entry in the Trio object. It does not upload anything and does not modify the existing writeCTD() path.

Usage

buildDatasetEvidenceSubmission(
  trio,
  datasetTaskID,
  evidenceName = names(trio$evidence),
  evidenceType = NA_character_
)

Arguments

trio

A Trio object.

datasetTaskID

Task identifier to link evidence rows to. Defaults to generated task IDs when not supplied.

evidenceName

Character vector of Trio evidence names to include. Defaults to all evidence in trio.

evidenceType

Either "columns" or "figshare" indicating where to find the evidence.

Value

A data.frame matching the proposed DatasetEvidence table schema. evidenceID is left as NA.

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."
)
buildDatasetEvidenceSubmission(
  trio,
  datasetTaskID = "task_001",
  evidenceType = "experimental_ground_truth"
)
#>              evidenceID datasetTaskID supportingEvidence is_in_data
#> class_labels       <NA>      task_001       class_labels       TRUE
#>              evidenceSourceID              evidenceType
#> class_labels             <NA> experimental_ground_truth