paramlink (version 1.1-5)

linkres: S3 methods for class 'linkres'.

Description

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

Usage

# S3 method for linkres
print(x, ...)
# S3 method for linkres
summary(object, ...)
# S3 method for linkres
as.data.frame(x, ..., sort = TRUE)
peakSummary(x, threshold, width = 1, physmap = NULL)
# S3 method for linkres
plot(x, chrom = NULL, ylim = NULL, ...)

Arguments

x, object

a linkres object (normally produced by lod or merlin).

…

further arguments.

sort

a logical, indicating if the data frame should be sorted according to map position.

threshold

a single numeric. A peak is defined as a regions of at least width consecutive markers LOD score above threshold.

width

a single numeric.

physmap

a matrix or data frame with three columns: Marker name, chromosome and physical position. This argument is optional.

chrom

NULL, or a numeric containing chromosome numbers. In the latter case only results for the markers on the indicated chromosomes will be plotted.

ylim

NULL, or a numeric of length 2: to be passed on to plot.default.

See Also

lod, merlin

Examples

# NOT RUN {
x = linkdat(toyped, model=1)
lods = lod(x, theta='max')
summary(lods)
as.data.frame(lods)

# }