Pedigree loops
Functions for identifying, breaking and restoring loops in pedigrees.
pedigreeLoops(x) breakLoops(x, loop_breakers = NULL, verbose = TRUE) tieLoops(x) findLoopBreakers(x) findLoopBreakers2(x)
x |
a |
loop_breakers |
either NULL (resulting in automatic selection of loop breakers) or a numeric containing IDs of individuals to be used as loop breakers. |
verbose |
a logical: Verbose output or not? |
Most of paramlink's handling of pedigree loops is done under the hood -
using the functions described here - without need for explicit action from
end users. When a linkdat object x is created, an internal routine
detects if the pedigree contains loops, in which case x$hasLoops is
set to TRUE. In analyses of x where loops must be broken (e.g. lod
score computation or marker simulation), this is done automatically by
calling breakLoops.
In some cases with complex inbreeding, it can be instructive to plot the pedigree after breaking the loops. Duplicated individuals are plotted with appropriate labels (see examples).
The function findLoopBreakers identifies a set of individuals
breaking all inbreeding loops, but not marriage loops. These require more
machinery for efficient detection, and paramlink does this is a seperate
function, findLoopBreakers2, utilizing methods from the igraph
package. Since this is rarely needed for most users, igraph is not
imported when loading paramlink, only when findLoopBreakers2 is
called.
In practice, breakLoops first calls findLoopBreakers and
breaks at the returned individuals. If the resulting linkdat object still
has loops, findLoopBreakers2 is called to break any marriage loops.
For breakLoops, a linkdat object in which the
indicated loop breakers are duplicated. The returned object will also have a
non-null loop_breakers entry, namely a matrix with the IDs of the
original loop breakers in the first column and the duplicates in the second.
For tieLoops, a linkdat object in which any duplicated
individuals (as given in the x$loop_breakers entry) are merged. For
any linkdat object x, the call tieLoops(breakLoops(x)) should
return x.
For pedigreeLoops, a list containing all inbreeding loops (not
marriage loops) found in the pedigree. Each loop is represented as a list
with elements 'top', a 'bottom' individual, 'pathA' (individuals forming a
path from top to bottom) and 'pathB' (creating a different path from top to
bottom, with no individuals in common with pathA). Note that the number of
loops reported here counts all closed paths in the pedigree and will in
general be larger than the genus of the underlying graph.
For findLoopBreakers and findLoopBreakers2, a numeric vector
of individual ID's.
Magnus Dehli Vigeland
x = cousinsPed(1, child=TRUE)
# Make the child affected, and homozygous for rare allele.
x = swapAff(x, 9)
x = setMarkers(x, marker(x, 9, c(2,2), alleles=1:2, afreq=c(0.99, 0.01)))
# Compute the LOD score under a recessive model. Loops are automatically broken in lod().
x = setModel(x, 2)
LOD1 = lod(x, theta=0.1)
stopifnot(round(LOD1, 2) == 0.88)
# Or we can break the loop manually before computing the LOD:
loopfree = breakLoops(x, loop_breaker=8)
plot(loopfree)
LOD2 = lod(loopfree, theta=0.1)
stopifnot(all.equal(x, tieLoops(loopfree)))
stopifnot(all.equal(LOD1, LOD2))
# Pedigree with marriage loop: Double first cousins
if(require('igraph')) {
y = doubleCousins(1, 1, child=TRUE)
findLoopBreakers(y) # --> 9
findLoopBreakers2(y) # --> 9 and 4
breakLoops(y) # uses both 9 and 4
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