SparseDCParams: The SparseDCParams class

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

The SparseDCParams class

Description

S4 class that holds parameters for the SparseDC simulation.

Parameters

The SparseDC simulation uses the following parameters:

nGenes

The number of genes to simulate in each condition.

nCells

The number of cells to simulate.

[seed]

Seed to use for generating random numbers.

markers.n

Number of marker genes to simulate for each cluster.

markers.shared

Number of marker genes for each cluster shared between conditions. Must be less than or equal to markers.n

.

[markers.same]

Logical. Whether each cluster should have the same set of marker genes.

clusts.c1

Numeric vector of clusters present in condition 1. The number of times a cluster is repeated controls the proportion of cells from that cluster.

clusts.c2

Numeric vector of clusters present in condition 2. The number of times a cluster is repeated controls the proportion of cells from that cluster.

[mean.lower]

Lower bound for cluster gene means.

[mean.upper]

Upper bound for cluster gene means.

The parameters not shown in brackets can be estimated from real data using sparseDCEstimate. For details of the SparseDC simulation see sparseDCSimulate.

Oshlack/splatter documentation built on Dec. 10, 2024, 3:48 p.m.