furcation-class {rehh} | R Documentation |
An S4 class representing the complete furcation pattern around a focal marker.
Description
An S4 class representing the complete furcation pattern around a focal marker.
Slots
.Data
a list containing for each allele an object of
allelefurcation-class
.mrk.name
the name/identifier of the focal marker.
position
the chromosomal position of the focal marker.
xlim
the range of marker positions.
nhap
the number of haplotypes in the sample.
See Also
Examples
# copy example files into working directory
make.example.files()
# read first example file
hh <- data2haplohh(hap_file = "example1.hap", map_file = "example1.map", allele_coding = "01")
# remove example files
remove.example.files()
# calculate furcation structure around marker "rs6"
f <- calc_furcation(hh, mrk = "rs6")
# extract left side tree of ancestral allele (which is coded by '0')
f[['0']]@left
# the tree consists of seven nodes, '1' being the root node
# nodes 2 and 3 have the root node as parent, etc.
# the first chromosome is attached as a label node to node 7, etc.
# For comparison, a plot of the complete furcation structure:
plot(f)
[Package rehh version 3.2.2 Index]