Retrieve an analysis specification from registry

Retrieves a fully-specified AnalysisSpec object from a Cohort's registry by name. Useful for accessing all properties of a registered analysis (description, path_template, key_cols, etc.).

Usage

analysis_spec(cohort, name)

Arguments

cohort: A Cohort object.
name: Character scalar with the name of the AnalysisSpec to retrieve.

Value

The AnalysisSpec object if found.

Details

Raises an informative error if the spec name is not found in the registry.

Examples

# Create and register a spec
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
)

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)

# Retrieve the spec
retrieved_spec <- analysis_spec(cohort_with_spec, "somatic_vars")
print(retrieved_spec@reader)  # "read_tsv"
#> [1] "read_tsv"