| relatednessCoeff {paramlink} | R Documentation |
Relatedness coefficients
Description
Computes inbreeding coefficients for all pedigree members, and Jacquard's condensed identity coefficients for any pair of members. These are simple wrappers for functions in other packages or external programs.
Usage
inbreeding(x)
kinship_coefs(x, ids = NULL)
jacquard(x, ids)
jacquard2(x, ids, verbose = FALSE, cleanup = TRUE)
Arguments
x |
a |
ids |
a integer vector of length 2. |
verbose |
a logical, indicating if messages from IdCoefs should be printed. |
cleanup |
a logical: If TRUE, the pedfile and sample file created for the IdCoefs run are deleted automatically. |
Details
Both inbreeding and kinship_coefs are thin wrappers of
kinship. jacquard2, executes an external
call to the C program IdCoefs (Abney, 2009). For this to
function, IdCoefs must be installed on the computer (see link in the
References section below) and the executable placed in a folder included in
the PATH variable. The jacquard2 wrapper works by writing the
necessary files to disk and calling IdCoefs via system.
Value
For inbreeding, a numerical vector with the inbreeding
coefficients, with names according to the ID labels x$orig.ids.
For kinship_coefs, either a single numeric (if ids is a pair
of pedigree members) or the whole kinship matrix, with x$orig.ids as
dimnames.
For jaquard and jaquard2, a numerical vector of
length 9 (in the standard order of Jacquard's condensed identity
coefficients).
References
The IdCoefs program: Abney, Mark (2009). A graphical
algorithm for fast computation of identity coefficients and generalized
kinship coefficients. Bioinformatics, 25, 1561-1563.
http://home.uchicago.edu/~abney/abney_web/Software.html
See Also
Examples
# Offspring of first cousins
x = cousinsPed(1, child=TRUE)
inb = inbreeding(x)
stopifnot(inb[9] == 1/16)
# if ID labels are not 1:9, care must be taken in extracting correct elements.
set.seed(1357)
y = relabel(x, sample(1:9))
child = leaves(y)
inbreeding(y)[child] #wrong
inb = inbreeding(y)[as.character(child)] #correct
inb
# the inbreeding coeff of the child equals the kinship coeff of parents
kin = kinship_coefs(y, parents(y, child))
stopifnot(inb==kin, inb==1/16)