linkedLR {KLINK}

LR with pairwise linked markers

Description

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

Usage

linkedLR(
  pedigrees,
  linkageMap,
  linkedPairs = NULL,
  maxdist = Inf,
  markerData = NULL,
  mapfun = "Kosambi",
  lumpSpecial = TRUE
)

Arguments

pedigrees

A list of two pedigrees.

linkageMap

A data frame with columns including Marker, Chrom and PosCM.

linkedPairs

A list of marker pairs. If not supplied, calculated as getLinkedPairs(markerData$Marker, linkageMap, maxdist = maxdist).

maxdist

A number, passed onto getLinkedMarkers() if linkedPairs is NULL.

markerData

A data frame with marker data, typically the output of markerSummary(pedigrees).

mapfun

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

lumpSpecial

A logical, by default TRUE.

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, KLINK::LINKAGEMAP)

# For testing
# .linkedLR(pedigrees, markerpair = c("SE33", "D6S474"), linkageMap = LINKAGEMAP)