paramlink (version 1.1-5)

examineKinships: Check pedigree for relationship errors

Description

This function provides a convenient way to check for pedigree errors in a linkage project or other situations where marker data is available for several members. The function calls IBDestimate to estimate IBD coefficients for all indicated pairs of pedigree members and produces a colour-coded plot where wrong relationships are easy to spot.

Usage

examineKinships(
  x,
  who = "all",
  interfam = c("founders", "none", "all"),
  makeplot = T,
  pch = 4,
  ...
)

Arguments

x

A linkdat object, or a list of such.

who

A character vector of one or more of the words 'parents', 'siblings', 'hugs' (= halfsibs/uncles/grandparents), 'cousins' and 'unrelated'. Two additional single-word values are possible: 'all' (all of the above, plus 'other') and 'close' (= 'parents', 'siblings', 'hugs', 'cousins').

interfam

A character; either 'founders', 'none' or 'all', indicating which interfamiliar pairs of individuals should be included. Only relevant if x is a list of several linkdat objects.

makeplot

A logical.

pch

Plotting symbol (default: cross).

…

Other plot arguments passed on to showInTriangle.

Value

A list of data.frames (one for each relation category) with IBD estimates.

See Also

IBDestimate, IBDtriangle, showInTriangle

Examples

# NOT RUN {
x = cousinsPed(1)
x = simpleSim(x, 500, alleles=1:2)
examineKinships(x)

# Pretend we didn't know the brothers (3 and 6) were related
x1 = branch(x, 3)
x2 = branch(x, 6)
x2$famid = 2

# Notice the error: An 'unrelated' dot close to the sibling point
examineKinships(list(x1, x2))

# }