simATACCount: The simATACCount class

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

Description

S4 class that holds parameters for the count matrix of simATAC simulation.

Parameters

simATAC simulation parameters:

nBins

The bin number to simulate.

nCells

The cell number to simulate.

[seed]

Seed to use for generating random numbers.

[default]

The logical variable whether to use default parameters (TRUE) or learn from data (FALSE)

[species]

An string indicating the species of the input cells. simATAC supports "hg38", "hg19", "mm9", and "mm10" in the current version.

[bin.coordinate.file]

The address of the file containing bins' coordinates including three columns in the format of "chr start end". The file must have a header of "chr start end" at the first line. If your data does not match the genome coordinates provided by simATAC, and you do not have the file containing bin information, use the "None" value.

Library size parameters

lib.mean1

Mean parameter for the first component of library size bimodal Gaussian distribution.

lib.mean2

Mean parameter for the second component of library size bimodal Gaussian distribution

lib.sd1

Standard deviation parameter for the first component of library size bimodal Gaussian distribution.

lib.sd2

Standard deviation parameter for the second component of library size bimodal Gaussian distribution.

lib.prob

Probability parameter for the first component in bimodal Gaussian distribution. The probability for the second component is 1-lib.prob.

Non-zero cell proportion parameters

non.zero.pro

The proportion of non-zero cells per bin in the original count matrix

mean.coef0

Estimated coefficient of power zero variable in the polynomial function

mean.coef1

Estimated coefficient of power one variable in the polynomial function

mean.coef2

Estimated coefficient of power two variable in the polynomial function

[noise]

[noise.mean]

Gaussian mean to be added as noise to the final simulated counts

[noise.sd]

Gaussian standard deviation to be added as noise to the final simulated counts

sparse.fac

Sparsit factor to be multiplied to the input of Poisson distribution on the final simulated count matrix

The parameters not shown in brackets can be estimated from real data using simATACEstimate. For details of the simATAC simulation see simATACSimulate.

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