Create an hsquared data container — hs

Usage

hs_data(
  phenotypes,
  pedigree = NULL,
  genotypes = NULL,
  markers = NULL,
  expression = NULL,
  annotation = NULL,
  annotation_id = NULL,
  environment = NULL,
  environment_id = NULL,
  id = "id"
)

Arguments

phenotypes: A data frame of phenotypic records.
pedigree: Optional pedigree data frame.
genotypes: Optional genotype matrix or data frame. Matrix row names or data-frame ID values identify individuals. When markers is supplied, genotype marker column names must match marker-map IDs exactly.
markers: Optional marker map data frame. When supplied, it must contain marker ID, chromosome, and position columns. Recognized aliases include marker, snp, or id; chromosome, chr, or chrom; and position, pos, bp, or base_pair.
expression: Optional expression matrix or data frame.
annotation: Optional annotation data frame.
annotation_id: Optional column name used to match annotation rows to expression feature columns. When supplied, the column must exist in annotation.
environment: Optional environment/covariate data frame.
environment_id: Optional column name used to match environment rows to phenotype records. When supplied, the column must exist in both phenotypes and environment.
id: Name of the individual ID column in phenotypes.

Value

An hs_data object.

Details

hs_data() collects phenotype, pedigree, genotype, marker, expression, annotation, and environment inputs into one checked container. It is a lightweight data-contract object for future genomic, QTL/eQTL, and multi-omics workflows. It does not fit models. The v0.1 parser can use an hs_data object directly as data, reading model variables from phenotypes and making named components such as pedigree available to formula terms.

summary(hs_data(...)) reports ID overlap diagnostics, pedigree diagnostics, and, when expression, genotype, or marker components are supplied, expression-feature, genotype-column, marker-map, and genotype-marker alignment diagnostics. When annotation_id is supplied, it reports expression-feature annotation coverage diagnostics. When environment_id is supplied, it also reports environment metadata coverage diagnostics.

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)
bundle
#> <hs_data>
#>   phenotypes: 3 rows
#>   phenotype IDs: 3
#>   pedigree IDs: 4
summary(bundle)
#> <summary_hs_data>
#>   components: phenotypes, pedigree
#>   phenotype IDs: 3
#>   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