Various utility functions for ped objects
pedsize(x)hasUnbrokenLoops(x)
hasInbredFounders(x, chromType = "autosomal")
hasSelfing(x)
hasCommonAncestor(x)
subnucs(x)
peelingOrder(x)
A ped object, or (in some functions - see Details) a list of such.
Either "autosomal" (default) or "x".
pedsize(x) returns the number of pedigree members in x
hasUnbrokenLoops(x) returns TRUE if x has loops, otherwise FALSE. (No
computation is done here; the function simply returns the value of
x$UNBROKEN_LOOPS).
hasInbredFounders(x) returns TRUE is founder inbreeding is specified
for x and at least one founder has positive inbreeding coefficient. See
founderInbreeding() for details.
hasSelfing(x) returns TRUE if the pedigree contains selfing events. This
is recognised by father and mother begin equal for some child. (Note that for
this to be allowed, the gender code of the parent must be 0.)
hasCommonAncestor(x) computes a logical matrix A whose entry A[i,j]
is TRUE if pedigree members i and j have a common ancestor in x, and FALSE
otherwise. By convention, A[i,i] is TRUE for all i.
subnucs(x) returns a list of all nuclear sub-pedigrees of x, wrapped as
nucleus objects. Each nucleus is a list with entries father, mother and
children.
peelingOrder(x) calls subnucs(x) and extends each entry with a link
individual, indicating a member linking the nucleus to the remaining
pedigree. One application of this function is the fact that if fails to
find a complete peeling order if and only if the pedigree has loops. (In fact
it is called each time a new ped object is created by ped() in order to
detect loops.) The main purpose of the function, however, is to prepare for
probability calculations in other packages, as e.g. in
pedprobr::likelihood.
The functions hasUnbrokenLoops(), hasInbredFounders() and
hasSelfing() allow as input either a single ped object or a list of
such. In the latter case each function returns TRUE if it is TRUE for any of
the components.
# NOT RUN {
x = fullSibMating(1)
stopifnot(pedsize(x) == 6)
stopifnot(hasUnbrokenLoops(x))
# All members have common ancestors except the grandparents
CA = hasCommonAncestor(x)
stopifnot(!CA[1,2], !CA[2,1], sum(CA) == length(CA) - 2)
# Effect of breaking the loop
y = breakLoops(x)
stopifnot(!hasUnbrokenLoops(y))
stopifnot(pedsize(y) == 7)
# A pedigree with selfing (note the necessary `sex = 0`)
z1 = singleton(1, sex = 0)
z2 = addChildren(z1, father = 1, mother = 1, nch = 1)
stopifnot(!hasSelfing(z1), hasSelfing(z2))
# Nucleus sub-pedigrees
stopifnot(length(subnucs(z1)) == 0)
peelingOrder(cousinPed(1))
# }
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