pedigree-class | R Documentation |
Objects of class "pedigree"
represent a set of
individuals that can have two parents including their parent-child
relations. The terminology has been taken from cattle breeding.
The "pedinbred"
class is an extension of the pedigree class
with an additional slot of the inbreeding coefficients.
Objects in the "pedigree"
class can be created by calls of the
form new("pedigree", ...)
, or more conveniently,
pedigree(sire= ., dam = ., label =.)
.
Objects of the "pedinbred"
class are created by coercing a
pedigree to class "pedinbred"
.
sire
:integer vector (with some NA
entries),
denoting a previous entry in the pedigree corresponding to
the current entry's “father”.
dam
:similarly as sire
for the “mother”
of each entry.
label
:a "character"
vector of the same length
as sire
and dam
giving a unique ID for the
corresponding entry.
F
:(class "pedinbred"
only) a numeric vector of
inbreeding coefficients.
signature(from = "pedigree", to = "sparseMatrix")
:
returns a sparse, unit lower-triangular matrix which is the inverse of the
"L" part of the "LDL'" form of the Cholesky factorization of the
relationship matrix. All non-zero elements below the diagonal
are -0.5.
signature(from = "pedigree", to = "data.frame")
: ...
signature(x = "pedigree")
: ...
signature(object = "pedigree")
: ...
signature(x = "pedigree")
: ...
R. A. Mrode, Linear Models for the Prediction of Animal Breeding Values, 2nd ed, CABI Publishing, 2005.
2010. A.I. Vazquez, D.M. Bates, G.J.M. Rosa, D. Gianola and K.A. Weigel. Technical Note: An R package for fitting generalized linear mixed models in animal breeding. Journal of Animal Science, 88:497-504.
pedigree
, inbreeding
## Rather use, pedigree()! The following is "raw code":
## Example from chapter 2 of Mrode (2005)
p1 <- new("pedigree",
sire = as.integer(c(NA,NA,1, 1,4,5)),
dam = as.integer(c(NA,NA,2,NA,3,2)),
label = as.character(1:6))
p1
(dtc <- as(p1, "sparseMatrix")) # T-inverse in Mrode's notation
solve(dtc)
inbreeding(p1)
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