simATACSimulate: simATAC simulation

In bowang-lab/simATAC: This package is a single-cell ATAC-seq simulator

Description

Simulate bin by cell count matrix from a sparse single-cell ATAC-seq bin by cell input using simATAC methods.

Usage

simATACSimulate(object = newsimATACCount(), verbose = TRUE, ...)

Arguments

object	simATACCount object with simulation parameters. See simATACCount for details.
verbose	Logical variable. Prints the simulation progress if TRUE.
...	Any additional parameter settings to override what is provided in simATACCount object.

Details

simATAC provides the option to manually adjust each of the simATACCount object parameters by calling setParameters. See examples for a demonstration of how this can be used.

The simulation involves the following steps:

1. Set up simulation parameters

2. Set default parameters if needed

3. Set up SingleCellExperiment object

4. Simulate library sizes

5. Simulate non zero entries

6. Simulate bin means

7. Create final synthetic counts

The final output is a SingleCellExperiment object that contains the simulated count matrix. The parameters are stored in the colData (for cell specific information), rowData (for bin specific information) or assays (for bin by cell matrix) slots. This additional information includes:

rowData

BinMean

The simulated bins' means.

colData

LibSize

The simulated library size values.

assays

counts

The sparse matrix containing simulated counts.

Code: https://github.com/bowang-lab/simATAC

Value

SingleCellExperiment object containing the simulated counts.

See Also

simATACSimLibSize, simATACSimZeroEntry, simATACSimBinMean, simATACSimTrueCount

bowang-lab/simATAC documentation built on Jan. 28, 2021, 1:22 a.m.