linkres: S3 methods for class 'linkres'.

In paramlink2: Parametric Linkage Analysis

S3 methods for class 'linkres'.

Description

Functions for printing, summarizing and plotting the results of a linkage analysis.

Usage

## 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, ...)

Arguments

x, object	A linkres object (normally produced by lod() or merlinLod()).
...	further arguments.
chrom	(Optional) A numeric indicating which chromosomes to be included in the plot.
lwd, type, ylim	Graphical parameters passed on to plot().
xlab, ylab	Axis labels.

Value

These functions are called for their side effects.

See Also

lod(), merlinLod(), lodPeaks()

Examples

# 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)

paramlink2 documentation built on Sept. 11, 2024, 6:48 p.m.