- x
A pedtools::ped object or a list of such.
- ids
A vector of ID labels from x. By default, the genotyped members
of x are used.
- extra
Either the word "parents" (default), or a non-negative integer.
See Details.
- alleleMatrix
A matrix with two columns for each marker. By default
extracted from x
- loci
A list of marker attributes. By default extracted from x.
- pedlist
A list of pedigrees to optimise over. If NULL, buildPeds()
is used to generate a list.
- inferPO
A logical. If TRUE, an initial stage of pairwise IBD
estimation is done to infer high-confidence parent/child pairs, and also
non-parent/child pairs. When this option is used, arguments to knownPO
and notPO are ignored.
- sex
A vector of the same length as labs, with entries 1 (male) or 2
(female).
- age
A numeric or character vector. If numeric, and age[i] < age[j],
then individual i will not be an ancestor of individual j. The numbers
themselves are irrelevant, only the partial ordering. (No inference is made
about individuals of equal age.) Alternatively, for finer control, age
may be a character vector of inequalities, e.g., age = c("1>2", "1>3").
- knownPO
A list of vectors of length 2, containing the ID labels of
pairs known to be parent-offspring. By default, both directions are
considered; use age to force a specific direction.
- knownSub
A ped object involving a subset of the labs individuals.
- allKnown
A logical. If TRUE, no other pairs than knownPO will be
assigned as parent-offspring. If FALSE (default), all pairs except those in
notPO are treated as potential parent-offspring.
- notPO
A list of vectors of length 2, containing the ID labels of pairs
known not to be parent-offspring.
- noChildren
A vector of ID labels, indicating individuals without
children of their own.
- connected
A logical. If TRUE (default), only connected pedigrees are
returned.
- maxInbreeding
A single numeric indicating the highest permitted
inbreeding coefficient. Default: 1/16 (as with first-cousin parents.)
- linearInb
A parameter controlling the maximum separation of linearly
related spouses. Either TRUE (allow all linear inbreeding), FALSE (disallow
all) or a non-negative integer. For example, linearInb = 1 allows
parent/child mating, but not grandparent/grandchild or more distant linear
relatives. Default: FALSE.
- sexSymmetry
A logical. If TRUE (default), pedigrees which are equal
except for the gender distribution of the added parents, are regarded as
equivalent, and only one of each equivalence class is returned. Example:
paternal vs. maternal half sibs.
- sortResults
A logical. If TRUE (default), the output is sorted so that
the most likely pedigree comes first.
- founderInb
A number in the interval [0,1], used as background
inbreeding level in all founders. Default: 0.
- numCores
A positive integer. The number of cores used in
parallelisation. Default: 1.
- verbose
A logical.