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Register an analysis specification in a cohort

Source: R/analysis_registry.R
analysis_register.Rd

Registers an AnalysisSpec in a Cohort's registry, enabling standardized access and discovery of analysis specifications. Returns a new Cohort object with the spec added (immutable update pattern).

Usage

analysis_register(cohort, spec)

Arguments

cohort

A Cohort object to update.

spec

An AnalysisSpec object to register. The spec name is used as the registry key.

Value

A new Cohort object with the spec added to the registry. If a spec with the same name already exists, it is replaced. Note that this follows the immutable S7 pattern: the original cohort is not modified.

Details

Validates that:

  • cohort is a Cohort object

  • spec is an AnalysisSpec object

See also

analysis_spec_new() for creating specs, analysis_list() for listing registered specs, analysis_spec() for retrieving a spec from registry

Examples

# Create a cohort
study <- study_new(study_id = "STUDY001", title = "My Study")
manifest <- data.frame(
  subject_id = c("S1", "S1", "S2", "S2"),
  species = c("rat", "rat", "rat", "rat"),
  assay = c("wes", "wes", "wes", "wes"),
  sample_id = c("WES_T1", "WES_N1", "WES_T2", "WES_N2"),
  role = c("tumor", "normal", "tumor", "normal")
)
parsed <- validate_manifest(manifest)
cohort <- cohort_new(
  subject_tbl = parsed$subject_tbl,
  sample_map = parsed$sample_map,
  study = study
)

# Create and register an analysis spec
spec <- analysis_spec_new(
  name = "somatic_vars",
  assay = "wes",
  level = "pair",
  format = "tsv",
  reader = "read_tsv",
  key_cols = c("pair_id")
)

cohort_with_spec <- analysis_register(cohort, spec)
print(analysis_list(cohort_with_spec))
#> # A tibble: 1 × 6
#>   name         assay level format reader   root_key
#>   <chr>        <chr> <chr> <chr>  <chr>    <chr>   
#> 1 somatic_vars wes   pair  tsv    read_tsv NA