simulateContamination {celda} | R Documentation

## Simulate contaminated count matrix

### Description

This function generates a list containing two count matrices – one for real expression, the other one for contamination, as well as other parameters used in the simulation which can be useful for running decontamination.

### Usage

    simulateContamination(
      C = 300,
      G = 100,
      K = 3,
      NRange = c(500, 1000),
      beta = 0.1,
      delta = c(1, 10),
      numMarkers = 3,
      seed = 12345
    )

### Arguments

`C` | Integer. Number of cells to be simulated. Default `300`.
`G` | Integer. Number of genes to be simulated. Default `100`.
`K` | Integer. Number of cell populations to be simulated. Default `3`.
`NRange` | Integer vector. A vector of length 2 that specifies the lower and upper bounds of the number of counts generated for each cell. Default `c(500, 1000)`.
`beta` | Numeric. Concentration parameter for Phi. Default `0.1`.
`delta` | Numeric or Numeric vector. Concentration parameter for Theta. If input as a single numeric value, symmetric values for beta distribution are specified; if input as a vector of lenght 2, the two values will be the shape1 and shape2 paramters of the beta distribution respectively. Default `c(1, 5)`.
`numMarkers` | Integer. Number of markers for each cell population. Default `3`.
`seed` | Integer. Passed to `with_seed`. For reproducibility, a default value of 12345 is used. If NULL, no calls to `with_seed` are made.

### Value

A list containing the `nativeMatirx` (real expression), `observedMatrix` (real expression + contamination), as well as other parameters used in the simulation.

### Author(s)

Shiyi Yang, Yuan Yin, Joshua Campbell

### Examples

    contaminationSim <- simulateContamination(K = 3, delta = c(1, 10))

[Package celda version 1.8.1 Index]