lod | R Documentation |
Calculates the singlepoint log of the odds (LOD) scores of a pedigree for the specified markers, assuming a fixed recombination rate between the disease and each marker locus.
lod(
x,
aff,
model,
rho = 0,
liability = NULL,
markers = NULL,
maxOnly = NA,
loopBreakers = NULL,
peelOrder = NULL,
verbose = FALSE
)
x |
A |
aff |
A vector naming the affected pedigree members, or a numeric vector
of length |
model |
A |
rho |
A number between 0 and 0.5 (inclusive); the hypothesised recombination ratio between the marker and the disease locus. |
liability |
NULL (default) or a vector of length |
markers |
A vector of marker names or indices referring to markers
attached to |
maxOnly |
a logical indicating whether only the maximum LOD score should be returned. By default this is always done if the number of markers is 1. |
loopBreakers |
A vector of ID labels indicating loop breakers. (Only relevant for inbred pedigrees.) |
peelOrder |
For internal use. |
verbose |
a logical: verbose output or not. |
The LOD score of a marker is defined as
LOD(\rho) = \log
\frac{L(\rho)}{L(0.5)}
where the
logarithms are base 10, and L(\rho)
denotes the likelihood of the
observed marker genotypes given a recombination ratio \rho
between the
marker and the disease locus.
The likelihoods are computed with the pedprobr package.
If the number of markers is 1, or if maxOnly = TRUE
, a single
number is returned.
Otherwise a linkres
object, which is basically a data frame with columns
CHROM
, MARKER
, MB
and LOD
.
Magnus Dehli Vigeland
linkres, merlinLod()
, diseaseModel()
, lodPeaks()
x = nuclearPed(2) |>
addMarker(geno = c("1/2", "1/1", "1/2", "1/2"))
aff = c(2,1,2,2)
model = diseaseModel(model = "AD")
lod(x, aff, model)
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