Convert a combined Trio submission to payload structure

This helper converts the output of buildTrioSubmission() into the nested list structure used by the JSON payload in the prototype submission script.

Usage

buildTrioSubmissionPayload(submission)

Arguments

submission

A submission object returned by buildTrioSubmission().

Value

A named list with a top-level payload entry ready for jsonlite::toJSON(..., auto_unbox = TRUE).

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."
)
submission <- buildTrioSubmission(
  trio = trio,
  dataset_args = list(
    dataType = "omics",
    dataModality = "transcriptomics",
    technology = "RNA-seq",
    tissue = "blood",
    status = "healthy"
  ),
  task_args = list(
    taskStage = "prediction",
    taskType = "classification",
    taskName = "class_prediction"
  ),
  evidence_task_map = c(class_labels = "class_prediction")
)
payload <- buildTrioSubmissionPayload(submission)
names(payload)
#> [1] "payload"          "submission_links"