lod: Two-point LOD score

Description

Calculates the two-point LOD scores of a pedigree for the specified markers. The recombination ratio between the disease and marker loci can be either fixed at specific values, or optimized.

Usage

lod(x, markers=seq_len(x$nMark), t=c(0, 0.1, 0.2, 0.5), tol=0.01, 
    max.only=FALSE, silent=max.only)

Arguments

a linkdat object.

markers

an integer vector denoting which markers to use.

either a numeric containing specific recombination ratio(s), or the word "max", indicating that the recombination ratio should be optimized by the program.

tol

a numeric passed on to optimize as its tolerance parameter.

max.only

a logical indicating whether only the maximum LOD score should be returned.

silent

a logical. The output is less verbose if TRUE.

Value

If max.only=FALSE, a linkres object, essentially a matrix containing the LOD scores. If t is numeric, the matrix has dimensions length(t), length(markers), and the entry in row t_0, column m_0 is the lod score of the pedigree for marker m_0 assumming a recombination rate of t_0. If t="max", the linkres matrix has one column per marker and two rows: The first containing the LOD score and the second the optimal recombination ratio for each marker. If a marker has incompatible values (i.e. if a child of homozygous 1/1 parents has a 2 allele), the corresponding matrix entries are NaN. If max.only=TRUE, only the highest LOD score is returned, as a numeric of length 1.

Details

The LOD score is defined as LOD(t) = log_10(L(t) - log_10(L(t=0.5), where L(t) denotes the likelihood of the observed pedigree data as a function of the recombination ratio t between the marker and the disease locus.

Examples

Run this code

data(toyped)
x = linkdat(toyped, model=1)
res_max = lod(x, max.only=TRUE)
res_def = lod(x)[1,1]
res_opt = lod(x, t="max")[1,1]

stopifnot(all(0.3 == round(c(res_max, res_def, res_opt), 1)))

data(dominant)
y = linkdat(dominant)
y = setModel(y, model=1, penetrances=c(.001, .9, .99))
lod(y, markers=305:310)
lod(y, markers=305:310, t="max")