Marker Genetics Module - Server Function

Reads an uploaded long-format marker genotype file (D1 format: id, locus, allele1, allele2), validates and pivots it (checkMarkerGenotypeFile, buildMarkerGenotypeMatrix), estimates marker-based kinship independent of pedigree (markerKinship), and surfaces a per-animal comparison of pedigree-based mean kinship (indivMeanKin, already computed upstream and passed in via kinshipMatrix) alongside the new marker-based mean kinship (markerMeanKin) – an independent check on the pedigree-implied relatedness, not a replacement for it. A second tab surfaces the heterozygosity diagnostic: per-animal observed heterozygosity (markerObservedHeterozygosity) alongside population-level expected heterozygosity (markerExpectedHeterozygosity). A third tab surfaces the Mendelian-exclusion parentage diagnostic (markerParentageExclusion): the pedigree's recorded dam/sire cross-referenced against the uploaded genotypes, flagging any recorded parent the genotype evidence contradicts. A fourth tab, "Cross- Center", surfaces a between-population differentiation statistic (markerFst) between the first uploaded file (implicitly "Center A") and a second, independently uploaded Center B genotype file – a population-level, two-dataset comparison, unrelated to the per-animal cross-center identity linking of resolveCrossCenterIds (Slice 4).

Usage

modMarkerGeneticsServer(id, kinshipMatrix, pedigree)

Arguments

id

character vector of length 1. Module namespace identifier.

kinshipMatrix

reactive returning the full pedigree-based kinship matrix (row and column names are animal IDs), or NULL while upstream analysis has not yet been run.

pedigree

reactive returning the current pedigree data frame (columns id, sire, dam), or NULL while upstream analysis has not yet been run.

Value

A list with eight reactive elements: markerGenotype, the raw uploaded genotype data frame (or NULL before upload); markerKinshipMatrix, the marker-based id x id kinship matrix (or NULL); comparisonTable, the per-animal indivMeanKin/markerMeanKin comparison data frame (or NULL); heterozygosityTable, the per-animal ho/he heterozygosity data frame (he is the population-wide mean expected heterozygosity, repeated per row) (or NULL); exclusionTable, the markerParentageExclusion flagged-pairs data frame (or NULL before a genotype file and a pedigree are both available); crossCenterGenotypeB, the raw uploaded Center B genotype data frame (or NULL before upload); crossCenterTable, the markerFst locus/fst data frame with a trailing "Pooled" row (or NULL before both center files are uploaded); and isReady, TRUE once comparisonTable has a value.

Details

This module never touches the existing single-locus genotype path (checkGenotypeFile/addGenotype/hasGenotype/ getGVGenotype/geneDrop) – the D1 long-format schema is a new, sibling concern.

See also

modMarkerGeneticsUI

Other Shiny modules: modBreedingGroupsServer(), modBreedingGroupsUI(), modGeneticDiversityServer(), modGeneticDiversityUI(), modGeneticValueServer(), modGeneticValueUI(), modGvAndBgDescServer(), modGvAndBgDescUI(), modInputServer(), modInputUI(), modMarkerGeneticsUI(), modORIPReportingServer(), modORIPReportingUI(), modPedigreeServer(), modPedigreeUI(), modPotentialParentsServer(), modPotentialParentsUI(), modPyramidServer(), modPyramidUI(), modSummaryStatsServer(), modSummaryStatsUI()