Export Entities from DNAnexus

Submits table-exporter jobs to export OFH data entities from the DNAnexus project. This function submits one job per entity using the DNAnexus table-exporter app with customizable parameters.

Usage

export_entities(
  dataset_or_cohort_or_dashboard = NULL,
  output_prefix = "ofh_raw_phenotype_data",
  output_format = "CSV",
  coding_option = "RAW",
  header_style = "FIELD-NAME",
  priority = "low",
  instance_type = "azure:mem2_ssd1_v2_x4",
  project_id = NULL,
  work_dir = "/",
  entities = NULL
)

Arguments

dataset_or_cohort_or_dashboard

Character string specifying the dataset, cohort, or dashboard to export data from (The record ID is required, e.g. "record-ABCD123456DEFG")

output_prefix

Character string specifying the prefix for output files

output_format

Character string specifying the output format (default "CSV")

coding_option

Character string specifying the coding option (default "RAW")

header_style

Character string specifying the header style (default "FIELD-NAME")

priority

Character string specifying job priority ("low", "normal", "high") (default "low")

instance_type

Character string specifying the DNAnexus instance type (default "azure:mem2_ssd1_v2_x4")

project_id

Character string specifying the DNAnexus project ID

work_dir

Character string specifying the working directory in DNAnexus the files should be exported to, defaults to project directory saved in chache (get_dx_cache("dx_path"))

entities

Character vector of entity names to export. If NULL (default), tries exports all possible OFH entities - entities not available will result in a failed job.

Value

NULL (side effect: submits DNAnexus jobs)

Examples

if (FALSE) { # \dontrun{
# Export all standard entities
# export_entities(
#   dataset_or_cohort_or_dashboard = "project-XXXXX:/my_dataset",
#   project_id = "project-XXXXX",
#   work_dir = "/exports"
# )
} # }