linkres | R Documentation |
Functions for printing, summarizing and plotting the results of a linkage analysis.
## S3 method for class 'linkres'
print(x, ...)
## S3 method for class 'linkres'
summary(object, ...)
## S3 method for class 'linkres'
plot(
x,
chrom = NULL,
type = "l",
lwd = NA,
ylim = NULL,
xlab = NULL,
ylab = NULL,
...
)
## S3 method for class 'linkres'
points(x, chrom = NULL, type = "l", lwd = NA, ...)
x , object |
A |
... |
further arguments. |
chrom |
(Optional) A numeric indicating which chromosomes to be included in the plot. |
lwd , type , ylim |
Graphical parameters passed on to |
xlab , ylab |
Axis labels. |
These functions are called for their side effects.
lod()
, merlinLod()
, lodPeaks()
# Pedigree with 5 simulated SNP markers
x = nuclearPed(3)
x = setMarkers(x, alleleMatrix = cbind(
m1 = c("1/1", "1/2", "1/2", "1/2", "1/2"),
m2 = c("1/2", "1/2", "1/2", "1/2", "1/2"),
m3 = c("1/1", "1/2", "1/2", "1/2", "1/1")), sep="/")
# Mother and all children affected
aff = c(1, 2, 2, 2, 2)
# LOD scores under autosomal dominant model
lods = lod(x, aff, model = diseaseModel(model = "AD"))
summary(lods)
as.data.frame(lods)
plot(lods)
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