furcation-class: An S4 class representing the complete furcation pattern...

In rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

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

calc_furcation

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)

rehh documentation built on Sept. 15, 2021, 5:06 p.m.