![[Experimental]](figures/lifecycle-experimental.svg)
Arguments
- data
An
hs_data()object.
Details
data_status() gives a direct user-facing view of the checks stored in an
hs_data() object. It reports component presence, ID overlap diagnostics,
pedigree diagnostics, expression-feature diagnostics, genotype-column
diagnostics, and marker-map/genotype-marker alignment diagnostics when those
inputs are supplied. When annotation_id is supplied, it reports
expression-feature annotation coverage diagnostics. When environment_id is
supplied, it also reports environment metadata coverage diagnostics. It does
not fit models, build genomic relationship matrices, add eQTL terms, or add
environment-effect terms.
Examples
ped <- data.frame(
id = c("a", "b", "c", "d"),
sire = c(NA, NA, "a", "a"),
dam = c(NA, NA, "b", "c")
)
dat <- data.frame(
y = c(1, 2, 3),
sex = c("f", "m", "f"),
id = c("a", "c", "d")
)
bundle <- hs_data(phenotypes = dat, pedigree = ped)
data_status(bundle)
#> <hs_data_status>
#> components: phenotypes, pedigree
#> ID overlap:
#> metric count
#> phenotype_ids 3
#> pedigree_ids 4
#> genotype_ids 0
#> expression_ids 0
#> phenotypes_without_pedigree 0
#> phenotypes_without_genotypes 3
#> genotypes_without_phenotypes 0
#> phenotypes_without_expression 3
#> expression_without_phenotypes 0
#> pedigree status:
#> metric count
#> pedigree_rows 4
#> pedigree_ids 4
#> phenotype_ids_with_pedigree 3
#> pedigree_only_ids 1
#> founders 2
#> nonfounders 2
#> known_sire_links 2
#> known_dam_links 2
#> missing_known_parent_ids 0
#> duplicate_pedigree_ids 0
#> self_parent_rows 0
#> same_known_parent_rows 0
#> expression status: not available
#> genotype status: not available
#> marker status: not available
#> annotation status: not available
#> environment status: not available