KLINK (version 1.1.0)

linkedLR: LR with pairwise linked markers

Description

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

Usage

linkedLR(
  pedigrees,
  linkageMap = map50,
  linkedPairs = NULL,
  maxdist = Inf,
  markerData = NULL,
  mapfun = "Kosambi",
  lumpSpecial = TRUE,
  alleleLimit = 10,
  verbose = TRUE,
  debug = FALSE
)

Value

A data frame with detailed LR results.

Arguments

pedigrees

A list of two pedigrees.

linkageMap

A data frame with columns including Marker, Chr and cM. By default, a built-in map norSTR::map50 of 50 STR markers is used.

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 indicating if special lumping should be activated. This is strongly recommended in all cases with linked STR markers.

alleleLimit

A number, by default 10, passed on to pedprobr::likelihood2().

verbose

A logical, by default TRUE.

debug

A logical, by default FALSE.

Examples

linkedLR(paternity)

# Detailed messages, including reports on lumping
linkedLR(paternity, debug = TRUE)

# For testing
# .linkedLR(paternity, markerpair = c("SE33", "D6S474"))