Package 'KLINK'

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 = map51,
  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::map51 of 51 STR markers is used.
linkedPairs	A list of marker pairs. If not supplied, calculated internally with getLinkedPairs().
maxdist	A number, passed onto getLinkedPairs() 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",
  checkLumping = TRUE,
  withParams = FALSE
)

Arguments

path	The path to a .fam file.
fallbackModel	The name of a mutation model; passed on to pedFamilias::readFam().
checkLumping	A logical. If TRUE (default), and if the pedigree disallows special lumping, unlumpable models are replaced with the fallback model.
withParams	A logical indicating if the Familias parameters should be included in the output. (See pedFamilias::readFam().)

Value

If withParams = FALSE, a list of two pedigree hypotheses in the form of ped objects. If withParams = TRUE, a list with components peds, params and hasUnlumpable.

Examples

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

loadFamFile(fam, withParams = TRUE)$params

---

Genetic map utilities

Description

Functions for loading, subsetting and pairing markers in genetic linkage maps.

Usage

loadMap(path)

getLinkedPairs(linkageMap = map51, maxdist = Inf)

subsetMap(linkageMap, markers)

Arguments

path	Path to a genetic map file, either a tab-separated text file or an Excel file with extension .xlsx.
linkageMap	A data frame with columns Marker, Chr, cM and (optionally) Mb, sorted by chromosome and position.
maxdist	A positive number indicating the maximum distance (in cM) between paired markers. Markers further apart are considered unlinked.
markers	A character vector of marker names to retain.

Details

loadMap() reads and sorts a genetic map from a text or Excel file, with required columns Marker, Chr, cM, and optionally a column Mb with physical positions used in karyograms.

subsetMap() restricts a map to a given set of markers. Marker names are matched flexibly, ignoring case and the separators "-", ".", "_" and space. The returned map uses the marker spelling supplied in markers. If multiple map entries match the same marker, only the first is retained.

getLinkedPairs() identifies disjoint marker pairs from the supplied map. Within each chromosome, pairs are selected greedily by successively choosing the closest available markers. Each marker occurs in at most one pair.

Value

loadMap() and subsetMap() return data frames. getLinkedPairs() returns a list of character vectors, each containing two marker names.

Examples

map = norSTR::map51

# Keep only markers present in a pedigree
mvec = pedtools::name(sibship[[1]])
map2 = subsetMap(map, mvec)

# Subsetting is insensitive to case and separators
mvec2 = sub(" ", ".", mvec) |> tolower()
subsetMap(map, mvec2)

# Pair the remaining markers
getLinkedPairs(map2, maxdist = 50)

---

Genetic marker maps

Description

These objects are re-exported from norSTR::map51 and norSTR::map50. map51 is the current map, while map50 is retained for reproducibility.

Usage

map51

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 (86.0 cM, 9 & 13 alleles)

• D5S818 and CSF1PO (26.2 cM, 9 & 11 alleles)

• vWA and D12S391 (11.4 cM, 12 & 23 alleles)

• D21S11 and Penta D (45.7 cM, 26 & 24 alleles)

(Genetic distances taken from the norSTR::map51 linkage map.)

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::map51
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)

---