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 = map50, maxdist = Inf)

Arguments

markers	A character vector containing marker names.
linkageMap	A data frame with columns including Marker, Chr and cM.
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 default map of 50 STR markers
map = norSTR::map50

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

---

Get LR totals

Description

Find, or add, the LR totals in a data frame with marker-wise LR values. The totals are found by multiplying the values in each column, after removing NA's.

Usage

getTotals(x, cols = c("LRlinked", "LRnolink", "LRnomut"))

addTotals(x, cols = c("LRlinked", "LRnolink", "LRnomut"))

Arguments

x	A data frame with LR results, typically the output of linkedLR().
cols	A vector of column names, by default c("LRlinked", "LRnolink", "LRnomut")

Details

Note that for the multiplication to respect linked markers, the input table should include LR values for only one marker in each linkage group, and NA's elsewhere. This is the format used by linkedLR().

Value

getTotals() returns a named numeric. addTotals returns a data frame equal to the input, but with a row of totals added at the bottom.

Examples

res = linkedLR(paternity)
getTotals(res)
addTotals(res)

---

Dataset for a case involving a putative half sibling.

Description

A list of two pedigrees forming opposing hypotheses about three individuals:

Usage

halfsib

Format

A list of two ped objects, named H1 and H2.

Details

• H1: A and B are full siblings, and C is their half brother

• H2: A and B are full siblings, and C is unrelated to them

The individuals are typed with 50 markers, but some genotypes are missing.

Examples

library(pedtools)
plotPedList(halfsib, hatched = typedMembers)
markerSummary(halfsib)
linkedLR(halfsib)

---

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)

---

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
)

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.

Value

A data frame with detailed LR results.

Examples

linkedLR(paternity)

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

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

---

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)

---

Load genetic map

Description

Loads a genetic map from a tab-separated text file, or from the first sheet of an Excel file with extension .xlsx.

Usage

loadMap(path)

Arguments

path	Path to the map file, either as plain text or Excel.

Details

The file should contain columns Marker, Chr and cM (slight variations in column names are allowed). Chromosomes should be positive integers, optionally prefixed by "chr". Positions must be nonnegative numeric values. Both period and comma are accepted as decimal separators.

Value

A data frame with standardised column names and rows sorted by chromosome and position.

Examples

tmp = tempfile(fileext = ".map")
map1 = as.data.frame(norSTR::map50)
write.table(map1, tmp, sep = "\t", quote = FALSE, row.names = FALSE)

map2 = loadMap(tmp)
stopifnot(all.equal(map1, map2))

---

Genetic marker map

Description

This object is re-exported from norSTR::map50.

Usage

map50

---

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)

---

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)

---

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 norSTR::norwayDB.

Usage

paternity

Format

A list of two pedigrees, named H1 and H2.

Examples

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

forrel::kinshipLR(paternity)

---

Dataset for a full vs half sibship case

Description

A list of two pedigrees forming opposing hypotheses about two individuals NN1 and NN2: FS (full siblings) vs. HS (half siblings). Both individuals are genotyped with the 23 markers included in the Fusion 6C kit. Among the 23 markers, four pairs are linked:

Usage

sibship

Format

A list of two ped objects, named FS and HS.

Details

• TPOX and D2S441 (88.8 cM, 9 & 13 alleles)

• D5S818 and CSF1PO (27.8 cM, 9 & 11 alleles)

• vWA and D12S391 (11.9 cM, 12 & 23 alleles)

• D21S11 and Penta D (44.7 cM, 26 & 24 alleles)

Examples

library(pedtools)
plotPedList(sibship, hatched = typedMembers)
markerSummary(sibship)
linkedLR(sibship)

---

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,
  hideEmpty = FALSE,
  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.
hideEmpty	A logical, indicating if untyped markers should be dropped.
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 = norSTR::map50
mdata = markerSummary(peds)

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

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

# openxlsx::openXL(tmp)

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