Relatedness coefficients by other programs
Wrappers for functions in other packages or external programs, computing various relatedness coefficients.
kinship2_kinship(x, ids = NULL) kinship2_kinshipX(x, ids = NULL) kinship2_inbreeding(x) kinship2_inbreedingX(x) idcoefs(x, ids) idcoefs2(x, ids, verbose = FALSE, cleanup = TRUE)
x |
A pedigree, in the form of 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. |
kinship2_inbreeding() and kinship2_kinship() are wrappers of
kinship2::kinship() with the parameter chrtype = "autosome".
Similarly ,kinship2_inbreedingX() and kinship2_kinshipX() wrap
kinship2::kinship() using chrtype = "x".
idcoefs() wraps identity::identity.coefs(), which is an R interface for
the C program IdCoefs written by Mark Abney (2009). The identity.coefs()
function sometimes causes R to crash, hence I have provided an alternative
wrapper, idcoefs2, which executes an external call to the original C
program IdCoefs (version 2.1.1). For this to work, 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
idcoefs2() wrapper works by writing the necessary files to disk and
calling IdCoefs via system().
For kinship2_inbreeding() and kinship2_inbreedingX(), a named
numerical vector with the inbreeding coefficients and ID labels as names.
For kinship2_kinship() and kinship2_kinshipX(), either a single numeric
(if ids is a pair of pedigree members) or the whole kinship matrix, with
the ID labels as dimnames.
For jaquard() and jaquard2(), a numerical vector of length 9 (in the
standard order of Jacquard's condensed identity coefficients).
Magnus Dehli Vigeland
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
# A random pedigree with 2 founders and 5 matings p = pedtools::randomPed(g = 5, founders = 2, seed = 111) # Check that ribd agrees with kinship2 package kinship_k2 = kinship2_kinship(p) kinship_ribd = kinship(p) stopifnot(identical(kinship_k2, kinship_ribd)) # Check on X also kinshipX_k2 = kinship2_kinshipX(p) kinshipX_ribd = kinshipX(p) stopifnot(identical(kinshipX_k2, kinshipX_ribd))
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