Validate a Cohort object

Checks the subject table, the sample map, and the link between them. cohort_new() calls this function after it builds the object. Call it directly to check a cohort that was built or changed by other means.

Usage

validate_cohort(x)

Arguments

x

A Cohort object.

Value

TRUE, invisibly, when the cohort is valid. Otherwise an error that lists every problem found.

Details

The checks are:

• x is a Cohort object.

• subject_tbl and sample_map are data frames.

• subject_tbl has the columns subject_id and species, both character, with no missing value. An empty string counts as missing. species is a free-form value; any organism is allowed.

• subject_tbl$subject_id has no duplicate.

• sample_map has the columns subject_id, assay, sample_id, and role, all character. The first three have no missing value.

• Every sample_map$subject_id exists in subject_tbl.

See also

cohort_new() for Cohort construction, validate_manifest() for manifest validation

Examples

subjects <- data.frame(
  subject_id = "RAT001",
  species = "rat",
  sex = "M"
)
samples <- data.frame(
  subject_id = "RAT001",
  assay = "wes",
  sample_id = "WES_R001",
  role = "tumor"
)
cohort <- cohort_new(
  subject_tbl = subjects,
  sample_map = samples
)

# cohort_new() already ran the checks. Run them again by hand.
validate_cohort(cohort)