| simulate_toy_gene_data {fastTopics} | R Documentation |
Simulate Toy Gene Expression Data
Description
Simulate gene expression data (UMI counts) under a toy expression model. Samples (expression profiles) are drawn from a multinomial topic model in which topics are "gene programs".
Usage
simulate_toy_gene_data(n, m, k, s)
Arguments
n |
The number of samples (gene expression profiles) to simulate. |
m |
The number of counts (genes) to simulate. |
k |
The number of topics ("gene programs") used to simulate the data. |
s |
A scalar specifying the total expression of each sample;
it specifies the "size" parameter in the calls to
|
Details
The mixture proportions are generated as follows. With probability 0.9, one proportion is one, or close to one, and the remaining are zero, or close to zero; that is, the counts are primarily generated from a single gene program. Otherwise (wtth probability 0.1), the mixture proportions are roughly equal.
Gene frequencies are drawn uniformly at random from [0,1].
Value
The return value is a list containing the counts matrix
X, and the gene frequencies F and mixture proportions
L used to generate the counts.