| founder.shared {MESS} | R Documentation |
Compute a common shared environment matrix
Description
Compute the common shared environment matrix for a set of related subjects. The function is generic, and can accept a pedigree, or pedigreeList as the first argument.
Usage
founder.shared(id, ...)
## S3 method for class 'pedigreeList'
founder.shared(id, ...)
## S3 method for class 'pedigree'
founder.shared(id, ...)
Arguments
id |
either a pedigree object or pedigreeList object |
... |
Any number of optional arguments. Not used at the moment |
Details
When called with a pedigreeList, i.e., with multiple families, the routine will create a block-diagonal-symmetric ‘bdsmatrix’ object. Since the [i,j] value of the result is 0 for any two unrelated individuals i and j and a ‘bdsmatix’ utilizes sparse representation, the resulting object is often orders of magnitude smaller than an ordinary matrix. When called with a single pedigree and ordinary matrix is returned.
Value
a matrix of shared environment coefficients
Author(s)
Claus Ekstrom claus@rprimer.dk
See Also
pedigree, kinship,
Examples
library(kinship2)
test1 <- data.frame(id =c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14),
mom =c(0, 0, 0, 0, 2, 2, 4, 4, 6, 2, 0, 0, 12, 13),
dad =c(0, 0, 0, 0, 1, 1, 3, 3, 3, 7, 0, 0, 11, 10),
sex =c(1, 2, 1, 2, 1, 2, 1, 2, 1, 1, 1, 2, 2, 2))
tped <- with(test1, pedigree(id, dad, mom, sex))
founder.shared(tped)