snp.sim.Q: Aternative SNPs simulation fn.

In caitiecollins/treeWAS: Phylogenetic tree-based microbial GWAS

Aternative SNPs simulation fn.

Description

NOT currently in use. Please use the regular snp.sim function to simulate genetic data.

Usage

snp.sim.Q(
  n.snps = 10000,
  n.subs = 1,
  snp.root = NULL,
  n.snps.assoc = 10,
  assoc.prob = 100,
  Q = matrix(c(2, 0.75, 0.75, 1, 3, 0.5, 0.25, 3, 3, 0.25, 0.5, 3, 1, 0.75, 0.75, 2),
    nrow = 4, byrow = T, dimnames = rep(list(c("0|0", "0|1", "1|0", "1|1")), 2)),
  tree = coalescent.tree.sim(100),
  n.phen.subs = 15,
  phen.loci = NULL,
  heatmap = FALSE,
  reconstruct = FALSE,
  dist.dna.model = "JC69",
  grp.min = 0.25,
  row.names = NULL,
  set = 3,
  seed = 1
)

Arguments

n.snps

An integer specifying the number of snps columns to be simulated.

Author(s)

Caitlin Collins [e-mail]

Examples

## Example ##

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