.synthesis {RScelestial}

Internal function for generating synthetic single-cell data through simulation of tumor growth and evolution.

Description

Internal function for generating synthetic single-cell data through simulation of tumor growth and evolution.

Usage

.synthesis(
  sample,
  site,
  evolutionSteps,
  mutationRate = 0.01,
  advantageIncreaseRatio = 1,
  advantageDecreaseRatio = 10,
  advantageKeepRatio = 100,
  advantageIncreaseStep = 0.01,
  advantageDecreaseStep = 0.01,
  mvRate = 0.5,
  fpRate = 0.2,
  fnRate = 0.1,
  seed = -1L
)

Arguments

sample

Number of samples

site

Number of sites

evolutionSteps

Number of non-root nodes in the evolutionary tree to be generated.

mutationRate

The rate of mutation on each evolutionary step in evolutionary tree synthesis.

advantageIncreaseRatio, advantageDecreaseRatio, advantageKeepRatio

A child node in the evolutionary tree is chosen for increase/decrease/keep its parent advantage with probabilities proportional to advantage.increase.ratio/advantage.decrease.ratio/advantage.keep.ratio.

advantageIncreaseStep, advantageDecreaseStep

The amount of increasing or decreasing the advantage of a cell relative to its parent.

mvRate

Rate of missing value to be added to the resulting sequences.

fpRate, fnRate

Rate of false positive (0 -> 1) and false negative (1 -> 0) in the sequences.

seed

The seed for randomization.

Value

The function returns a list. The list consists of

• sequence: A data frame representing result of sequencing. The data frame has a row for each locus and a column for each sample.

• true.sequence: The actual sequence for the sample before adding errors and missing values.

• true.clone: A list that stores index of sampled cells for each node in the evolutionary tree.

• true.tree: The evolutionary tree that the samples are sampled from. It is a data frame with src, dest, and len columns representing source, destination and weight of edges of the tree, respectively.