View source: R/examineKinships.R
examineKinships | R Documentation |
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.
examineKinships( x, who = "all", interfam = c("founders", "none", "all"), makeplot = T, pch = 4, ... )
x |
A |
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 |
makeplot |
A logical. |
pch |
Plotting symbol (default: cross). |
... |
Other plot arguments passed on to |
A list of data.frames (one for each relation category) with IBD estimates.
IBDestimate
, IBDtriangle
,
showInTriangle
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))
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