simulateContaminatedMatrix {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

    simulateContaminatedMatrix(C = 300, G = 100, K = 3, NRange = c(500,
      1000), beta = 0.5, delta = c(1, 2), seed = 12345)

### Arguments

`C` | Integer. Number of cells to be simulated. Default to be 300.
`G` | Integer. Number of genes to be simulated. Default to be 100.
`K` | Integer. Number of cell populations to be simulated. Default to be 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 to be c(500, 1000).
`beta` | Numeric. Concentration parameter for Phi. Default to be 0.5.
`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.
`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 object containing the real expression matrix and contamination expression matrix as well as other parameters used in the simulation.

### Examples

    contaminationSim <- simulateContaminatedMatrix(K = 3, delta = c(1, 9))
    contaminationSim <- simulateContaminatedMatrix(K = 3, delta = 1)

[Package celda version 1.0.4 Index]