Check data against existing IDs — check_complete

If data is an addition to an existing study, check the specimen and individual IDs against the master table of existing IDs. Contributors should upload the complete metadata files, so all IDs in the master table should be present in the uploaded data.

check_complete_ids(
  data,
  samples_table,
  study,
  id_type = c("individualID", "specimenID"),
  assay = NULL,
  success_msg = "Data includes a complete set of IDs",
  fail_msg = "Some IDs are missing from the data"
)

Arguments

data	Data frame of data to be checked
samples_table	Data frame containing master table of all individual and specimen IDs per study
study	Name of the study
id_type	`"individualID"` or `"specimenID"`
assay	String naming the assay. If provided, will filter `master_table` to the specific study and assay. This is useful when validating assay metadata in studies wheere multiple assays with different specimens were conducted. If `NULL` (the default), will look at all IDs for the study, regardless of assay.
success_msg	Message indicating the check succeeded.
fail_msg	Message indicating the check failed.

Value

A condition object indicating whether the required columns were present ("check_pass") or absent ("check_fail")

Examples

samples_table <- tibble::tribble(
  ~individualID, ~specimenID, ~study, ~assay,
  "A", "a1", "study1", "rnaSeq",
  "A", "a2", "study1", "rnaSeq",
  "B", "b1", "study1", "rnaSeq",
  "B", "b2", "study1", "rnaSeq",
  "B", "b1", "study1", "rnaSeq",
  "B", "b1", "study1", "rnaSeq",
  "C", "c1", "study1", "LC-MS",
  "D", "d1", "study2", "rnaSeq",
  "D", "d2", "study2", "rnaSeq"
)
dat <- tibble::tribble(
  ~individualID, ~specimenID,
  "A", "a1",
  "A", "a2"
)
check_complete_ids(
  data = dat,
  samples_table = samples_table,
  id_type = "individualID",
  study = "study1"
)
#> <error/check_fail>
#> Some IDs are missing from the data