simulateDataPhylo: Simulate the Data using the tree

In csoneson/compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods

Simulate the Data using the tree

Description

Use the Phylogenetic Poisson Log Normal model to simulate the data.

Usage

simulateDataPhylo(
  count_means,
  count_dispersions,
  tree,
  prop.var.tree,
  model.process = "BM",
  selection.strength = 0
)

Arguments

tree	a dated phylogenetic tree of class phylo with 'samples.per.cond * 2' species.
prop.var.tree	the proportion of the common variance explained by the tree for each gene. It can be a scalar, in which case the same parameter is used for all genes. Otherwise it needs to be a vector with length n.vars. Default to 1.
model.process	the process to be used for phylogenetic simulations. One of "BM" or "OU", default to "BM".
selection.strength	if the process is "OU", the selection strength parameter.

Value

Z a matrix with the data

csoneson/compcodeR documentation built on Nov. 3, 2024, 6:05 a.m.