make_DEG_pattern {Corbi}

Simulate differentially expressed gene pattern

Description

Generate complicated differentially expressed gene (DEG) pattern to simulate varied degree of heterogeneity.

Usage

make_DEG_pattern(
  n.genes,
  n.samples,
  fold.change = 2,
  gene.rate = 0.3,
  sample.rate = 1,
  active.rate = 1,
  up.rate = 0.5
)

Arguments

n.genes

The total number of genes in the simulated data.

n.samples

The total number of samples in the simulated data.

fold.change

The fold change level of DEGs.

gene.rate

The proportion of DEGs to all genes.

sample.rate

The proportion of abnormal samples to all samples.

active.rate

The probability that a DEG is truely differentially expressed in an abnormal sample.

up.rate

The proportion of up-regulated DEGs to all DEGs.

Details

The heterogeneity of gene expression pattern is mainly controlled by two parameters: sample.rate and active.rate. If both parameters are equal to 1, the gene expression pattern will be homogeneous, otherwise heterogeneous.

Value

This function will return a list with the following components:

FC

The matrix of simulated fold changes. Each row represents a gene and each column represents a sample.

gene

The vector of gene status: 1 for up-regulated, -1 for down-regulated, and 0 for normal genes.

sample

The vector of sample status: 1 for abnormal, and 0 for normal samples.