linkedLR {KLINK}R Documentation

LR with pairwise linked markers

Description

This function does the main LR calculations of the KLINK app.

Usage

linkedLR(pedigrees, linkageMap, markerData = NULL, mapfun = "Kosambi")

Arguments

pedigrees

A list of two pedigrees.

linkageMap

A data frame with columns including Pair, Marker, Chrom, PosCM

markerData

A data frame, normally extracted automatically from pedigrees.

mapfun

Name of the map function to be used; either "Haldane" or "Kosambi" (default)

Value

A data frame with detailed LR results.

Examples

library(forrel)

ped1 = nuclearPed(fa = "AF", child = "CH") |>
  profileSim(markers = NorwegianFrequencies)

ped2 = singletons(c("AF", "CH")) |>
  transferMarkers(from = ped1, to = _)

pedigrees = list(ped1, ped2)

linkedLR(pedigrees, LINKAGEMAP)


[Package KLINK version 0.7.3 Index]