Genetic Value Analysis Module - Server Function

Genetic Value Analysis Module - Server Function

Usage

modGeneticValueServer(
  id,
  pedigree,
  speciesOverrides = reactive(NULL),
  twinRelations = reactive(NULL)
)

Arguments

id

character vector of length 1. Module namespace identifier.

pedigree

reactive returning pedigree data frame.

speciesOverrides

reactive returning the user-configurable species overrides loaded at boot by loadSpeciesOverrides (a list with breedingTable, gestationTable, breedingAgeDefault, gestationDefault), or NULL. Threaded into reportGV. Defaults to reactive(NULL) so no config file means bundled behavior.

twinRelations

reactive returning a validated twin/zygosity sidecar data.frame (id1, id2, code), or NULL. Unlike the kinship-override file (uploaded through this module's own UI), this data does not originate inside this module – it is uploaded on the Pedigree Browser's Diagram tab and threaded in by appServer (BL-N Slice 3), so a declared MZ-twin pair's corrected kinship is reflected in reportGV's output regardless of which tab the user visits first. Defaults to reactive(NULL) (no twins declared).

Value

List with geneticValues, topAnimals, nAnalyzed, kinshipMatrix, kinshipOverrides (the validated kinship-override data frame loaded through this module's kinship-override upload, or NULL when none is loaded or it cannot be read), founderStats, maleFounders, femaleFounders, and snapshotSource (issue #167 Slice 4: the most recent run's analyzed pedigree, its nprcgenekeeprGV object, and its guIter/guThresh, captured atomically for modSnapshotTrendsServer, plus reportArgs (issue #170 Slice 3): the other nine settings the run passed to reportGV – the species tables and their defaults, the kinship overrides, the twin pairs and the three ranking cutoffs – so the rows built for earlier dates match the analysis beside them).

References

Lacy, R.C. (1989) Zoo Biology, 8, 111-123.

See also

modGeneticValueUI

modBreedingGroupsServer for using results.

Other Shiny modules: modBreedingGroupsServer(), modBreedingGroupsUI(), modCrossCenterIdentityServer(), modCrossCenterIdentityUI(), modDeidentifiedExportServer(), modDeidentifiedExportUI(), modGeneticDiversityServer(), modGeneticDiversityUI(), modGeneticValueUI(), modGvAndBgDescServer(), modGvAndBgDescUI(), modInputServer(), modInputUI(), modMarkerGeneticsServer(), modMarkerGeneticsUI(), modMatePairServer(), modMatePairUI(), modORIPReportingServer(), modORIPReportingUI(), modPedigreeServer(), modPedigreeUI(), modPotentialParentsServer(), modPotentialParentsUI(), modPyramidServer(), modPyramidUI(), modSnapshotTrendsServer(), modSnapshotTrendsUI(), modSummaryStatsServer(), modSummaryStatsUI()