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,
linkedPairs = NULL,
maxdist = Inf,
markerData = NULL,
mapfun = "Kosambi",
lumpSpecial = TRUE
)
Arguments
pedigrees |
A list of two pedigrees. |
linkageMap |
A data frame with columns including |
linkedPairs |
A list of marker pairs. If not supplied, calculated as
|
maxdist |
A number, passed onto |
markerData |
A data frame with marker data, typically the output of
|
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)
[Package KLINK version 1.0.0 Index]