simulateObservedMatrix: This function generates a list containing two count matrices...

In compbiomed/celda: CEllular Latent Dirichlet Allocation

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

simulateObservedMatrix(C = 300, G = 100, K = 3, N.Range = 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
N.Range	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 / 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 set.seed(). Default to be 12345

Examples

contamination.sim =  simulateObservedMatrix(  K=3,  delta=c(1,9)) 
contamination.sim =  simulateObservedMatrix(  K=3,  delta = 1) 

compbiomed/celda documentation built on May 25, 2019, 3:58 a.m.