Description Usage Arguments Details Value Author(s) See Also Examples
Calculates various forms of pedigree likelihoods.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16  likelihood(x, ...)
## S3 method for class 'linkdat'
likelihood(x, locus1, locus2 = NULL, theta = NULL,
startdata = NULL, eliminate = 0, logbase = NULL, loop_breakers = NULL,
...)
## S3 method for class 'singleton'
likelihood(x, locus1, logbase = NULL, ...)
## S3 method for class 'list'
likelihood(x, locus1, locus2 = NULL, ..., returnprod = TRUE)
likelihood_LINKAGE(x, marker, theta = NULL, afreq = NULL, logbase = NULL,
TR.MATR = NULL, initialCalc = NULL, singleNum.geno = NULL,
loop_breakers = NULL)

x 
a 
... 
further arguments. 
locus1 
a 
locus2 
either NULL, the character 'disease', or a

theta 
the recombination rate between locus1 and locus2 (in

startdata 
for internal use. 
eliminate 
mostly for internal use: a nonnegative integer indicating
the number of iterations in the internal genotypecompatibility algorithm.
Positive values can save time if 
logbase 
a numeric, or NULL. If numeric the loglikelihood is
returned, with 
loop_breakers 
a numeric containing IDs of individuals to be used as
loop breakers. If NULL, automatic selection of loop breakers will be
performed. See 
returnprod 
a logical; if TRUE, the product of the likelihoods is returned, otherwise a vector with the likelihoods for each pedigree in the list. 
marker 
an integer between 0 and 
afreq 
a numeric containing the marker allele frequencies. 
TR.MATR, initialCalc, singleNum.geno 
for internal use, speeding up linkage computations with fewallelic markers. 
All likelihoods are calculated using the ElstonStewart algorithm.
If locus2 = NULL
, the result is simply the likelihood of the
genotypes observed at the marker in locus1.
If locus2 = 'disease'
, the result is the likelihood of the marker
genotypes in locus1, given the affection statuses of the pedigree members,
the disease model and the recombination rate theta
between the marker
and disease loci. The main use of this is for computation of LOD scores in
parametric linkage analysis.
If locus2
is a marker object, the result is the likelihood of the
genotypes at the two markers, given the recombination rate theta between
them.
The function likelihood_LINKAGE
is a fast version of
likelihood.linkdat
in the case where locus2 = 'disease'
and
the marker in locus1 has less than 5 alleles.
The likelihood of the data. If the parameter logbase
is a
positive number, the output is log(likelihood, logbase)
.
Magnus Dehli Vigeland
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15  x = linkdat(toyped, model=1) #dominant model
lod1 = likelihood_LINKAGE(x, marker=1, theta=0, logbase=10) 
likelihood_LINKAGE(x, marker=1, theta=0.5, logbase=10)
lod2 = lod(x, markers=1, theta=0)
# these should be the same:
stopifnot(identical(lod1, as.numeric(lod2)), round(lod1, 2)==0.3)
# likelihood of inbred pedigree (grandfather/granddaughter incest)
y = addOffspring(addDaughter(nuclearPed(1, sex=2), 3), father=1, mother=5, 1)
m = marker(y, 1, 1, 6, 1:2)
l1 = likelihood(y, m)
l2 = likelihood(y, m, loop_breaker=5) # manual specification of loop_breaker
stopifnot(l1==0.09375, l2==l1)

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