fwd.coalescent.sim: Short one-phrase description.

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

Short one-phrase description.

Description

Longer proper discription of function...

Usage

fwd.coalescent.sim(
  n.ind = 100,
  n.snps = 10000,
  n.subs = 1,
  n.snps.assoc = 10,
  n.subs.assoc = 15,
  p = 1,
  heatmap = FALSE,
  reconstruct = FALSE,
  dist.dna.model = "JC69",
  seed = 1
)

Arguments

n.ind	An integer specifying the number of individual genomes to simulate (ie. the number of terminal nodes in the tree).
n.snps	An integer specifying the number of genetic loci to simulate.
n.subs	Either an integer or a vector (containing a distribution) that is used to determine the number of substitutions to occur on the phylogenetic tree for each genetic locus (see details).
n.snps.assoc	An optional integer specifying the number of genetic loci
heatmap	A logical indicating whether to produce a heatmap of the genetic distance between the simulated genomes of the n.ind individuals.
reconstruct	Either a logical indicating whether to attempt to reconstruct a phylogenetic tree using the simulated genetic data, or one of c("UPGMA", "nj", "ml") to specify that tree reconstruction is desired by one of these three methods (Unweighted Pair Group Method with Arithmetic Mean, Neighbour-Joining, Maximum-Likelihood).
seed	An optional integer controlling the pseudo-random process of simulation. Two instances of coalescent.sim with the same seed and arguments will produce identical output.
assoc.prob	An optional integer (> 0, <= 100) specifying the strength of the association between the n.snps.assoc loci and the phenotype (see details).
n.phen.subs	An integer specifying the expected number of phenotypic substitutions to occur on the phylogenetic tree (through the same process as the n.subs parameter when n.subs is an integer (see details)).
phen	An optional vector containing a phenotype for each of the n.ind individuals if no phenotypic simulation is desired.

Details

#### n.subs #### If the value of the n.subs parameter is set to an integer, this integer is used as the parameter of a Poisson distribution from which the number of substitutions to occur on the phylogenetic tree is drawn for each of the n.snps simulated genetic loci. If n.subs is a vector containing a distribution, this is used directly (in proportion to n.snps) to define the number of substitutions per site. For example, if n.subs=c(3000, 900, 70, 20, 0, 10) and n.snps=8000, then 6000 simulated sites will undergo exactly one substitution somewhere on the phylogenetic tree, 1800 will undergo two, 140 three, 40 four, 0 five, and 20 six. #### assoc.prob #### The assoc.prob parameter controls the strength of association through a process analagous to dilution. All n.snps.assoc loci are initially simulated to undergo a substitution every time the phenotype undergoes a substitution (ie. perfect association). The assoc.prob parameter then acts like a dilution factor, removing (100 - assoc.prob) of the substitutions that occurred during simulation under perfect association.

Author(s)

Caitlin Collins [e-mail]

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