gd: Genetic distance matrix

In seedy: Simulation of Evolutionary and Epidemiological Dynamics

Description

Given a set of genomic samples, returns a pairwise geentic distance matrix

Usage

gd(samp, libr, nuc, key)

Arguments

samp	Vector of sample IDs.
libr	Library object from simulation functions. A list in which each entry represents a unique genotype, and is a vector of mutated nucleotide positions relative to the reference seqeunce.
nuc	Nucleotide database from simulation functions. A list (corresponding to libr) in which each entry represents a unique genotype, and is a vector of mutated nucleotides relative to the reference sequence.
key	Vector of sample IDs in the order they appear in the libr and nuc objects.

Details

Each element of samp represents one row and column in the genetic distance matrix.

Value

Returns a symmetric genetic distance matrix with rows and columns corresponding to the samp vector.

Examples

data(withinhost)
gd(withinhost$obs.strain, withinhost$libr, withinhost$nuc, withinhost$librstrains)

seedy documentation built on May 29, 2017, 10:58 a.m.