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.
simulateContamination( C = 300, G = 100, K = 3, NRange = c(500, 1000), beta = 0.1, delta = c(1, 10), numMarkers = 3, seed = 12345 )
C | Integer. Number of cells to be simulated. Default |
---|---|
G | Integer. Number of genes to be simulated. Default |
K | Integer. Number of cell populations to be simulated.
Default |
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
|
beta | Numeric. Concentration parameter for Phi. Default |
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 |
numMarkers | Integer. Number of markers for each cell population.
Default |
seed | Integer. Passed to |
A list containing the nativeMatirx
(real expression),
observedMatrix
(real expression + contamination), as well as other
parameters used in the simulation.
Shiyi Yang, Yuan Yin, Joshua Campbell