Build a Dataset submission row from a Trio object

This helper is the first step in the new submission workflow. It does not upload anything and does not modify the existing writeCTD() path.

Usage

buildDatasetSubmission(
  trio,
  name = private_submission_dataset_name(trio),
  dataType,
  dataModality,
  technology,
  description = trio$description,
  doi = NA_character_,
  organism = NA_character_,
  tissue,
  status
)

Arguments

trio

A Trio object.

name

Dataset name for submission. Defaults to the existing Trio name, falling back to trio$dataSourceID when needed.

dataType

One of "omics" or "clinical".

dataModality

One of "genomics", "transcriptomics", "epigenomics", "proteomics", "metabolomics", "patient", or "other".

technology

Free-text technology description.

description

Dataset description. Defaults to trio$description if present.

doi

DOI reference for the dataset.

organism

Free-text organism label.

tissue

Free-text tissue label.

status

One of "healthy", "diseased", "developmental", or "other".

Value

A one-row data.frame matching the proposed Dataset table schema. datasetID is left as NA because it is expected to be generated by the submission backend.

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."
)
buildDatasetSubmission(
  trio,
  dataType = "omics",
  dataModality = "transcriptomics",
  technology = "RNA-seq",
  tissue = "blood",
  status = "healthy"
)
#>   datasetID            name source    datasourceID dataType    dataModality
#> 1      <NA> example_dataset   <NA> example_dataset    omics transcriptomics
#>   technology              description  doi numSamples organism tissue  status
#> 1    RNA-seq A small example dataset. <NA>          3     <NA>  blood healthy