markerSimParametric | R Documentation |
This function simulates genotypes for two individuals given their IBD distribution, for N identical markers.
markerSimParametric( kappa = NULL, delta = NULL, states = NULL, N = 1, alleles = NULL, afreq = NULL, seed = NULL, returnValue = c("singletons", "alleles", "genotypes", "internal") )
kappa |
A probability vector of length 3, giving a set of realised kappa coefficients (between two noninbred individuals). |
delta |
A probability vector of length 9, giving a set of condensed identity coefficients (Jacquard coefficients). |
states |
An integer vector of length |
N |
A positive integer: the number of independent markers to be simulated. |
alleles |
A vector with allele labels. If NULL, the following are tried in order:
|
afreq |
A numeric vector with allele frequencies, possibly named with allele labels. |
seed |
An integer seed for the random number generator (optional). |
returnValue |
Either "singleton" (default) or "alleles". (see Value). |
Exactly one of kappa
, delta
and states
must be given; the other two
should remain NULL.
If states
is given, it explicitly determines the condensed identity state
at each marker. The states are described by integers 1-9, using the tradition
order introduced by Jacquard.
If kappa
is given, the states are generated by the command states = sample(9:7, size = N, replace = TRUE, prob = kappa)
. (Note that identity
states 9, 8, 7 correspond to IBD status 0, 1, 2, respectively.)
If delta
is given, the states are generated by the command states = sample(1:9, size = N, replace = TRUE, prob = delta)
.
The output depends on the value of the returnValue
parameter:
"singletons": a list of two singletons with the simulated marker data attached.
"alleles": a list of four vectors of length N
, named a
, b
, c
and
d
. These contain the simulated alleles, where a/b and c/d are the
genotypes of the to individuals.
"genotypes": a list of two vectors of length N
, containing the
simulated genotypes. Identical to paste(a, b, sep = "/")
and paste(c, d, sep = "/")
, where a
, b
, c
, d
are the vectors returned when
returnValue == "alleles"
.
"internal": similar to "alleles", but using the index integer of each allele. (This option is mostly for internal use.)
# MZ twins markerSimParametric(kappa = c(0,0,1), N = 5, alleles = 1:10) # Equal distribution of states 1 and 2 markerSimParametric(delta = c(.5,.5,0,0,0,0,0,0,0), N = 5, alleles = 1:10) # Force a specific sequence of states markerSimParametric(states = c(1,2,7,8,9), N = 5, alleles = 1:10)
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