simulate_count: Simulate a random UMI count matrix

In mauranolab/decal: Differential Expression Analysis of Clonal Alterations Local effects

Description

It generates a random UMI count matrix based on DECAL model assumptions given the cells total count (depth) and gene prevalence ratio (ratio of genes UMIs over the total; ratio). Alternatively, you can further specify the generative model, by giving a log2 fold-change (lfc) effect and each gene dispersion (theta).

Usage

sim_count(depth, ratio, lfc = 0L, theta = 100L)

sim_count_from_data(reference, lfc = 0, theta = 100L, ngenes = NULL)

Arguments

depth	simulated cells total UMI count
ratio	ratio of genes UMI to be simulated
lfc	log2 fold-change effect to be applied to the simulated cells
theta	genes' dispersion parameter
reference	a count matrix to base the simulation
ngenes	number of genes to be simulated. When NULL it replicates the gene ratio found in reference, otherwise it simulates ngenes with ratio ranging in a logarithm scale from lowest to highest observed ratio observed.

Value

random UMI count matrix

mauranolab/decal documentation built on Dec. 21, 2021, 3:50 p.m.