Returns a tibble with one row per registered AnalysisSpec in a Cohort. Summarizes key metadata for quick inspection of available analyses.
Value
A tibble with the following columns:
name: Analysis name (chr)assay: Assay type (chr)level: Data level - "subject", "pair", or "cohort" (chr)format: File format (chr)reader: Reader function name (chr)root_key: Optional root path key (chr)
If the cohort has no registered specs, returns an empty tibble with these columns.
Details
The returned tibble includes only the most essential metadata fields
for discovery and filtering. Use analysis_spec() to retrieve the
full AnalysisSpec object including description, path_template, and
key_cols.
See also
analysis_register() for registering specs,
analysis_spec() for retrieving a full spec object
Examples
# Create and register specs
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
)
spec1 <- analysis_spec_new(
name = "somatic_vars",
assay = "wes",
level = "pair",
format = "tsv",
reader = "read_tsv",
key_cols = c("pair_id")
)
spec2 <- analysis_spec_new(
name = "gene_expr",
assay = "scrna",
level = "subject",
format = "rds",
reader = "readRDS",
key_cols = c("subject_id")
)
cohort <- analysis_register(cohort, spec1)
cohort <- analysis_register(cohort, spec2)
analysis_list(cohort)
#> # A tibble: 2 × 6
#> name assay level format reader root_key
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 somatic_vars wes pair tsv read_tsv NA
#> 2 gene_expr scrna subject rds readRDS NA