KersplatParams: The KersplatParams class

In splatter: Simple Simulation of Single-cell RNA Sequencing Data

Description

S4 class that holds parameters for the Kersplat simulation.

Parameters

The Kersplat simulation uses the following parameters:

nGenes

The number of genes to simulate.

nCells

The number of cells to simulate.

[seed]

Seed to use for generating random numbers.

Mean parameters

mean.shape

Shape parameter for the mean gamma distribution.

mean.rate

Rate parameter for the mean gamma distribution.

mean.outProb

Probability that a gene is an expression outlier.

mean.outFacLoc

Location (meanlog) parameter for the expression outlier factor log-normal distribution.

mean.outFacScale

Scale (sdlog) parameter for the expression outlier factor log-normal distribution.

mean.dens

density object describing the log gene mean density.

[mean.method]

Method to use for simulating gene means. Either "fit" to sample from a gamma distribution (with expression outliers) or "density" to sample from the provided density object.

[mean.values]

Vector of means for each gene.

Biological Coefficient of Variation parameters

bcv.common

Underlying common dispersion across all genes.

[bcv.df]

Degrees of Freedom for the BCV inverse chi-squared distribution.

Network parameters

[network.graph]

Graph containing the gene network.

[network.nRegs]

Number of regulators in the network.

Paths parameters

[paths.programs]

Number of expression programs.

[paths.design]

data.frame describing path structure. See kersplatSimPaths for details.

Library size parameters

lib.loc

Location (meanlog) parameter for the library size log-normal distribution, or mean parameter if a normal distribution is used.

lib.scale

Scale (sdlog) parameter for the library size log-normal distribution, or sd parameter if a normal distribution is used.

lib.dens

density object describing the library size density.

[lib.method]

Method to use for simulating library sizes. Either "fit" to sample from a log-normal distribution or "density" to sample from the provided density object.

Design parameters

[cells.design]

data.frame describing cell structure. See kersplatSimCellMeans for details.

Doublet parameters

[doublet.prop]

Proportion of cells that are doublets.

Ambient parameters

[ambient.scale]

Scaling factor for the library size log-normal distribution when generating ambient library sizes.

[ambient.nEmpty]

Number of empty cells to simulate.

The parameters not shown in brackets can be estimated from real data using kersplatEstimate. For details of the Kersplat simulation see kersplatSimulate.

splatter documentation built on Dec. 3, 2020, 2:01 a.m.