Summary Statistics Module - Server Function

Server logic for summary statistics module displaying genetic analysis results including kinship statistics, histograms, box plots, and relationship designation analysis.

Usage

modSummaryStatsServer(
  id,
  geneticValues,
  pedigree,
  kinshipMatrix = NULL,
  founderStats = NULL
)

Arguments

id

character vector of length 1. Module namespace identifier.

geneticValues

reactive returning genetic value analysis results. Must be a data frame with columns id, meanKinship, and genomeUniqueness. Optional zScore column enables z-score plots.

pedigree

reactive returning pedigree data frame with columns id, sire, dam, and sex. Optionally gen.

kinshipMatrix

optional reactive returning kinship matrix. If NULL, the module will calculate kinship from the pedigree.

founderStats

optional reactive returning a list of founder statistics (fe, fg, total, nMaleFounders, nFemaleFounders). When supplied, a founder summary table is rendered on the Summary Statistics tab (monolith parity). If NULL, it is omitted.

Value

A list with reactive components:

• summaryData - Summary statistics (nAnimals, meanMK, meanGU)

• relationships - Pairwise relationship designations from convertRelationships()

• relationClasses - Relationship class frequency table from makeRelationClassesTable()

• firstOrderCounts - First-order relative counts per animal from countFirstOrder()

• mkSummary - Six-number summary of mean kinship

• guSummary - Six-number summary of genome uniqueness

Details

This module provides:

• Summary statistics (counts, mean kinship, genome uniqueness)

• Histograms and box plots for genetic value distributions

• Relationship classification using convertRelationships()

• Relationship class frequency tables using makeRelationClassesTable()

• First-order relative counts using countFirstOrder()

• Export functionality for kinship matrix, founders, and relationships

See also

modSummaryStatsUI for the user interface

convertRelationships for relationship classification

makeRelationClassesTable for relationship class summary

countFirstOrder for first-order relative counting

kinship for kinship matrix calculation