Description Objects from the Class Slots Methods References See Also Examples

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.

- coerce
`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.- coerce
`signature(from = "pedigree", to = "data.frame")`

: ...- head
`signature(x = "pedigree")`

: ...- show
`signature(object = "pedigree")`

: ...- tail
`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.

1 2 3 4 5 6 7 8 9 10 | ```
## 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)
``` |

pedigreeTools documentation built on May 31, 2017, 3:19 a.m.

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