Genomic and QTL formula markers — genomic

Usage

genomic(formula, G = NULL, Ginv = NULL, markers = NULL, ...)

single_step(
  formula,
  H = NULL,
  Hinv = NULL,
  pedigree = NULL,
  markers = NULL,
  group = NULL,
  Gamma = NULL,
  tau = 1,
  omega = 1,
  blend_weight = 0,
  ridge = 0,
  ...
)

markers(M, model = c("random", "fixed", "scan"), ...)

marker_scan(M, map = NULL, ...)

qtl_scan(position, genotype_probs = NULL, ...)

Arguments

formula: A random-effect expression such as 1 | id.
G, Ginv, H, Hinv: Relationship or precision matrices for future genomic and single-step models.
markers: An individual-by-marker numeric dosage matrix with rows named by genotyped ID. Entries must be the biallelic allele count 0/1/2 (or an imputed dosage in the closed interval [0, 2]); a matrix in the centered -1/0/1 convention must be recoded (add 1) before it is passed in. A 0/1 panel of homozygous inbred lines (as in BGLR::wheat) must be doubled to 0/2 before it is passed in; hsquared does not recode it. For genomic(), the engine uses sample allele frequencies, VanRaden method 1, and ridge 0.01. For single_step(), this is the genotyped-subset marker matrix used to construct the genomic relationship.
...: Reserved for future syntax.
pedigree: A pedigree data frame (id, sire, dam) for the single-step H^-1 construction path (single_step(1 | id, pedigree = ped, markers = M)), in place of a precomputed Hinv.
group: Animal-to-metafounder group labels for the future H^Gamma single-step path; must be supplied together with Gamma.
Gamma: A supplied metafounder relationship matrix for the future H^Gamma single-step path; supplied, not estimated, and must be supplied together with group.
tau, omega, blend_weight, ridge: Single-step construction tuning knobs (Aguilar et al. 2010); defaults tau = omega = 1, blend_weight = ridge = 0.
M: A marker or dosage matrix for future marker-effect and scan models.
model: Planned marker-effect mode.
map: A marker map for future marker scans.
position: A chromosome-position table or variable for future QTL scans.
genotype_probs: Genotype probabilities for future interval/QTL scans.

Value

NULL, invisibly. Calls are interpreted by hsquared() when they appear inside model formulas.

Details

These functions provide readable formula vocabulary for genomic, single-step, marker-effect, GWAS, and QTL/eQTL models. Called directly they are inert (they return NULL); they take meaning only inside an hsquared() formula. genomic() fits a narrow Gaussian REML random-intercept model only through the explicit engine = "julia", target = "genomic" path. single_step() also remains opt-in and experimental. The reported genomic coefficient is sigma_g2 / (sigma_g2 + sigma_e2) on the declared relationship scale, not generally an average marginal phenotypic-variance fraction or pedigree/population heritability. For genomic(1 | id, markers = M), the engine fits the ridged kernel K = G + 0.01 I. Genomic variance and the REML log-likelihood match the unridged VanRaden G model; the reported residual is the residual of K, equal to the residual on G minus 0.01 * sigma_g2. The ratio therefore differs from the textbook GREML ratio on G. To compare residual variance with other software, add 0.01 * sigma_g2 back. The marker-built ridge is fixed at 0.01; genomic() has no ridge argument (ridge exists only on single_step()). A supplied Ginv is used as given. Accepted genomic forms are genomic(1 | id, Ginv = Ginv) or genomic(1 | id, markers = M) (GREML, or SNP-BLUP via target = "snp_blup"), and single_step(1 | id, Hinv = Hinv) (a precomputed inverse) or single_step(1 | id, pedigree = ped, markers = M) (the engine constructs H^-1 from the pedigree + genotyped-subset markers via target = "single_step_construct"). Adding group plus supplied Gamma fits a supplied-Gamma, validation-scale H^Gamma path through target = "metafounder_single_step"; Gamma is supplied, not estimated. When data is an hs_data() container that bundles a pedigree and genotypes, single_step(1 | id) resolves both from the bundle (the animal(1 | id) precedent), so neither pedigree = nor markers = is required; explicit arguments override the bundle. The remaining markers (markers(), marker_scan(), qtl_scan()) are still inert syntax reservations that the parser rejects with a planned-not-implemented message.