Generate differentially expressed gene (DEG) data from negative binomial distribution.
make_DEG_data2(
n.genes,
n.samples.A,
n.samples.B,
exp.mean = 8,
exp.sd = 2,
dispersion = NULL,
size.factor.sd = 0.1,
...
)The total number of genes in the simulated data.
The number of samples in the group A.
The number of samples in the group B.
The mean of log-normal distribution that determines gene-specific expression mean.
The standard deviation of log-normal distribution that determines gene-specific expression mean.
The dispersion parameter for negative binomial distribution. The default values are determined by the expression mean.
The standard deviation of size factors for samples.
The parameters passed to function make_DEG_pattern.
This function will return a list with the following components:
The matrix of simulated DEG pattern, which is generated by make_DEG_pattern.
The expression matrix of group A. Each row represents a gene and each column represents a sample.
The expression matrix of group B. Each row represents a gene and each column represents a sample.
The expression values of each gene are assumed following a negative binomial distribution with
gene-specific mean, which follows a log-normal distribution. The size factor for each
sample follows a Gaussian distribution with zero mean and specific standard deviation.
The heterogeneity of gene expression data is simulated by using the function make_DEG_pattern.