dist_0.01: Nsubs per site with limited recombination (R = 0.01; M =...

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

Nsubs per site with limited recombination (R = 0.01; M = 0.01).

Description

This vector contains a homoplasy distribution, representing the relative number of substitutions per site that occurred along a phylogenetic tree when evolution was simulated with a mutation rate of M = 0.01 and a recombination rate of R = 0.01 (r/m = 1).

Usage

data(dist_0.01)

Format

A named vector of length 15.

Details

A per-site mutation rate of M = 0.01 indicates that each site, on average, undergoes 0.01 substitutions due to mutation along the phylogenetic tree. A per-site recombination rate of R = 0.01 indicates that each site, on average, undergoes 0.01 substitutions per site due to within-species recombination.

Each element of the vector indicates the number of genetic loci that have undergone the number of substitutions indicated by the name of that element (Nsub = i).

If visualised as a bar plot (with barplot(dist_0.01)), one would see that the Nsub distribution is arranged as if it were the counts of a histogram with index names along the x-axis, corresponding to Nsub (the number of substitutions per site), and cell counts along the y-axis, showing Nloci (the number of genetic sites undergoing Nsub=i substitutions along the tree).

Author(s)

Caitlin Collins [e-mail]

caitiecollins/treeWAS documentation built on March 9, 2024, 3:15 p.m.