Create a Cohort object

Builds a Cohort from a subject table and a sample map, with an optional Study, file paths, and analysis tables. The two tables are usually the output of validate_manifest().

Usage

cohort_new(
  subject_tbl,
  sample_map,
  study = NULL,
  paths = list(),
  analyses = list()
)

Arguments

subject_tbl

A data frame with one row per subject. Required columns: subject_id and species, both character. Other columns are kept as given.

sample_map

A long-format data frame with one row per sample. Required columns: subject_id, assay, sample_id, role, all character.

study

A Study object, or NULL. Defaults to NULL.

paths

Named list of file paths to data files or result folders. Defaults to an empty list.

analyses

Named list of analysis tables or other data objects. Defaults to an empty list.

Value

A Cohort object. An error when the tables fail validate_cohort().

Details

The steps are:

1. Check that subject_tbl and sample_map are data frames.

2. Convert both to tibbles.

3. Build the Cohort.

4. Run validate_cohort().

The function does not build Subject objects. Use subject() to read one subject from the cohort when an object is needed.

See also

validate_manifest() for preparing input tables, validate_cohort() for the checks, subject() for reading one subject, Study for study metadata

Examples

study <- study_new(
  study_id = "STUDY001",
  title = "Cross-species study",
  assays = c("WES", "snRNA-seq")
)

# A long-format manifest: one row per sample
manifest <- data.frame(
  subject_id = c("RAT001", "RAT001", "MOUSE1", "MOUSE1"),
  species = c("rat", "rat", "mouse", "mouse"),
  sex = c("M", "M", "F", "F"),
  assay = c("wes", "scrna", "wes", "atac"),
  sample_id = c("WES_T1", "RNA_1", "WES_T2", "ATAC_1"),
  role = c("tumor", "tumor", "tumor", NA)
)

parsed <- validate_manifest(manifest)
cohort <- cohort_new(
  study = study,
  subject_tbl = parsed$subject_tbl,
  sample_map = parsed$sample_map
)
print(cohort)
#> 
#> ── Cohort: Cross-species study 
#> • 2 subjects (1 mouse, 1 rat)
#> • 4 samples (2 wes, 1 atac, 1 scrna)

# Read one subject as a Subject object
subject(cohort, "RAT001")
#> Subject <RAT001>: rat