simulateCellTypes: Simulate expression profiles of specific cell-types.

In RaikOtto/artdeco: Alikeness Based on Regression on Transciptome DECOnvolution

Description

simulateCellTypes simulates in silico expression profiles of specific cell-types using a negative binomial distribution. Simulation is based on biological data and marker genes of these cell-types.

Usage

simulateCellTypes(
    referenceCellTypes,
    markerGenes,
    numSamples,
    seed,
    verbose
)

Arguments

referenceCellTypes	Matrix of single-cell expression values of the cell-type to be simulated. Used to estimate parameters for negative binomial distribution. Samples as columns and genes as rows. Counts have to be normalized beforehand.
markerGenes	Character vector containing marker genes which characterize the cell-type to be simulated. Gene identifiers need to be consistend with referenceCellTypes.
numSamples	An integer specifing the number of samples to be simulated.
seed	An integer specifing seed for simulation. Default is NULL. Random seed will be generated if no seed is provided.
verbose	Logical, indicating whether status updates will be printed. Default is TRUE.

Value

Matrix with simulated count values. Samples as columns and genes as rows.

RaikOtto/artdeco documentation built on Nov. 3, 2021, 6:18 p.m.