Package 'KLINK'

Identify linked marker pairs

Description

This function returns a "maximal" set of disjoint pairs of linked markers, given a genetic marker map and a subset of the markers included in the map. The pairs are identified in a greedy manner, successively choosing the closest markers on each chromosome.

Usage

getLinkedPairs(markers, linkageMap, maxdist = Inf)

Arguments

markers	A character vector containing marker names.
linkageMap	A data frame with columns including Marker, Chrom and PosCM.
maxdist	A positive number indicating the maximum linkage distance (in cM). Markers further apart than this are considered unlinked.

Value

A list of character vectors, each containing two marker names.

Examples

# Example using the built-in map of 50 STR markers
map = KLINK::LINKAGEMAP

getLinkedPairs(map$Marker, map, maxdist = 25)

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Launch KLINK

Description

This launches the KLINK app. runKLINK() is a synonym for launchApp(), but with an additional argument version.

Usage

launchApp()

runKLINK(version = NULL)

Arguments

version

A character, e.g. "1.0.0". If the installed version of KLINK differs from this, the program aborts with an error.

Value

No return value, called for side effects.

Examples

## Not run: 
launchApp()

## End(Not run)

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Built-in linkage map

Description

A genetic map including 50 autosomal STR markers.

Usage

LINKAGEMAP

Format

A data frame with 50 rows and 4 columns: Marker, Kit, Chrom, PosCM.

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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)

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Load .fam file

Description

Load .fam file

Usage

loadFamFile(path, fallbackModel = "equal", withParams = FALSE)

Arguments

path	The path to a .fam file.
fallbackModel	The name of a mutation model; passed on to pedFamilias::readFam().
withParams	A logical indicating if the Familias parameters should be included in the output. (See pedFamilias::readFam().)

Value

A list of two ped objects.

Examples

fam = system.file("extdata/halfsib-test.fam", package = "KLINK")
peds = loadFamFile(fam)
pedtools::plotPedList(peds)

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Generate table of marker data

Description

Generate table of marker data

Usage

markerSummary(pedigrees, replaceNames = FALSE)

Arguments

pedigrees	A list of 2 pedigrees.
replaceNames	A logical, indicating if IDs should be changed to Person1, Person2, ...

Value

A data frame.

Examples

markerSummary(paternity)

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Parse XML file associated with .fam file

Description

Parse XML file associated with .fam file

Usage

parseXML(xml)

Arguments

xml	Path to a file with extension .xml.

Examples

# (No example included)

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Dataset for a paternity case

Description

A list of two pedigrees forming the hypotheses in a paternity case: H1 (AF is the father of CH) and H2 (unrelated). AF and CH are genotyped with 11 markers, with allele frequencies from forrel::NorwegianFrequencies.

Usage

paternity

Format

A list of two pedigrees, named H1 and H2.

Examples

pedtools::plotPedList(paternity, marker = "SE33")
markerSummary(paternity)

forrel::kinshipLR(paternity)

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Write data and results to Excel

Description

This function produces an Excel document containing the genotype data and various LR tables.

Usage

writeResult(
  resultTable,
  pedigrees,
  linkageMap,
  markerData,
  outfile,
  notes = NULL,
  famname = NULL,
  settings = NULL,
  XML = NULL
)

Arguments

resultTable	A data frame.
pedigrees	A list of two ped objects.
linkageMap	A data frame.
markerData	A data frame.
outfile	The output file name.
notes	A character vector.
famname	The name of the input .fam file.
settings	A list of KLINK settings to be included in the output
XML	Optional data from .xml file.

Examples

# Built-in dataset `paternity`
peds = paternity
map = LINKAGEMAP
mdata = markerSummary(peds)

# Result table
LRtab = linkedLR(pedigrees = peds, linkageMap = map, markerData = mdata)

# Write to excel
tmp = paste0(tempfile(), ".xlsx")
writeResult(LRtab,
            pedigrees = peds,
            linkageMap = map,
            markerData = mdata,
            outfile = tmp)

# openxlsx::openXL(tmp)

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