Uploading methylation data to the DataSHIELD backends

du.upload.methyl.clocks(
  upload = TRUE,
  cohort_id,
  action = du.enum.action()$ALL,
  methyl_data_input_path = "",
  covariate_data_input_path = "",
  dict_version = "1_1",
  data_version = "16",
  data_format = du.enum.input.format()$CSV,
  dna_source = du.enum.dna.source()$CORD_BLOOD,
  norm_method = du.enum.norm.method()$RAW,
  run_mode = du.enum.run.mode()$NORMAL,
  database_name = "opal_data",
  override_project = NULL
)

Arguments

upload	do we need to upload the DataSHIELD backend
cohort_id	cohort name from the dictonary
action	action to be performed, can be 'populate' or 'all'
methyl_data_input_path	path to the methylation data
covariate_data_input_path	path to the covariate data to measure the age
dict_version	version of the dictionary
data_version	is the mean age (this needs to be a number)
data_format	can be CSV or RData
dna_source	can be 'cord_blood', 'peripheral_blood' or 'placenta'
norm_method	can be RAW=0, BMIQ=1, DASEN=2, SWAN=3, SQN=4, RCP=5, NOOB=6, CPACOR=7, FUNNORM=8, OTHER=9 (needs to be a number)
run_mode	can be NORMAL, NON_INTERACTIVE or TEST
database_name	is the name of the data backend of DataSHIELD, default = opal_data
override_project	override the generated project name

Examples


if (FALSE) {
du.upload.methyl.clocks(
  cohort_id = 'gecko',
  methyl_data_input_path = "~/path-to-file",
  covariate_data_input_path = "~/path-to-file",
  dna_source = 'placenta',
  norm_method = 0,
  dict_version = "2_2",
  data_version = "1",
  override_project = "custom_project_1_0"
)
}