ftree-class: An S4 class to represent a furcation tree on one side of one...

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

Description

An S4 class to represent a furcation tree on one side of one allele of a focal marker

Details

A furcation structure consists of two trees ("left" and "right") for each allele of a focal marker. If there are only bi-allelic markers and no missing values, the trees are bifurcating.

Missing values are treated similarly to an extra allele in so far as they cause a furcation. However, the resulting daughter node is marked accordingly and the chromosomes excluded from further calculations. If all chromosomes of a parent node have missing values, the "furcation" is degenerated and yields a single daughter node.

Note that a tree with n leaves can have at most 2n-1 nodes.

In a furcation tree, the leaves do not necessarily represent single chromosomes, either due to multiple missing data or because the first/last marker was reached before all extended haplotypes were distinct.

Slots

node_parent

a vector, representing the tree structure. Each node (number) is assigned its parent node (number).

node_pos

a vector, assigning to each node (number) its position in the chromosome, i.e. at which marker position the furcation occurred.

node_with_missing_data

a vector of type logical. Pseudo-furcations arise due to missing data at a marker. The daughter node (number) is marked accordingly.

label_parent

a vector, that attaches an "extra leave", representing the haplotype number (defined by the order in the haplotype data file) to leaves of the tree. This is necessary because in general not all leaves of the original tree represent a single haplotype/chromosome.

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