paramlink: examineKinships – R documentation

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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 color-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.

Author(s)

Magnus Dehli Vigeland

Examples

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))

paramlink

Parametric Linkage and Other Pedigree Analysis in R

v1.1-2

GPL (>= 2)

Authors

Magnus Dehli Vigeland [aut, cre], Thore Egeland [ctb], Guro Doerum [ctb]

Initial release

2018-01-05