BASiCS_Sim: Generates synthetic data according to the model implemented...

In catavallejos/BASiCS: Bayesian Analysis of Single-Cell Sequencing data

Generates synthetic data according to the model implemented in BASiCS

Description

BASiCS_Sim creates a simulated dataset from the model implemented in BASiCS.

Usage

BASiCS_Sim(Mu, Mu_spikes = NULL, Delta, Phi = NULL, S, Theta, BatchInfo = NULL)

Arguments

Mu	Gene-specific mean expression parameters \mu_i for all biological genes (vector of length q.bio, all elements must be positive numbers)
Mu_spikes	\mu_i for all technical genes defined as true input molecules (vector of length q-q.bio, all elements must be positive numbers). If Mu_spikes = NULL, the generated data will not contain spike-ins. If Phi = NULL, Mu_spikes will be ignored. Default: Mu_spikes = NULL.
Delta	Gene-specific biological over-dispersion parameters \delta_i, biological genes only (vector of length q.bio, all elements must be positive numbers)
Phi	Cell-specific mRNA content normalising parameters \phi_j (vector of length n, all elements must be positive numbers and the sum of its elements must be equal to n). Phi must be set equal to NULL when generating data without spike-ins. If Mu_spikes = NULL, Phi will be ignored. Default: Phi = NULL
S	Cell-specific technical normalising parameters s_j (vector of length n, all elements must be positive numbers)
Theta	Technical variability parameter \theta (must be positive). Theta can be a scalar (single batch of samples), or a vector (multiple batches of samples). If a value for BatchInfo is provided, the length of Theta must match the number of unique values in BatchInfo.
BatchInfo	Vector detailing which batch each cell should be simulated from. If spike-ins are not in use, the number of unique values contained in BatchInfo must be larger than 1 (i.e. multiple batches are present).

Value

An object of class SingleCellExperiment, including synthetic data generated by the model implemented in BASiCS.

Author(s)

Catalina A. Vallejos [e-mail], Nils Eling

References

Vallejos, Marioni and Richardson (2015). PLoS Computational Biology.

Examples

# Simulated parameter values for 10 genes
# (7 biogical and 3 spike-in) measured in 5 cells
Mu <- c(8.36, 10.65, 4.88, 6.29, 21.72, 12.93, 30.19)
Mu_spikes <-  c(1010.72, 7.90, 31.59)
Delta <- c(1.29, 0.88, 1.51, 1.49, 0.54, 0.40, 0.85)
Phi <- c(1.00, 1.06, 1.09, 1.05, 0.80)
S <- c(0.38, 0.40, 0.38, 0.39, 0.34)
Theta <- 0.39

# Data with spike-ins, single batch
Data <- BASiCS_Sim(Mu, Mu_spikes, Delta, Phi, S, Theta)
head(SingleCellExperiment::counts(Data))
dim(SingleCellExperiment::counts(Data))
altExp(Data)
rowData(altExp(Data))

# Data with spike-ins, multiple batches
BatchInfo <- c(1,1,1,2,2)
Theta2 <- rep(Theta, times = 2)
Data <- BASiCS_Sim(Mu, Mu_spikes, Delta, Phi, S, Theta2, BatchInfo)

# Data without spike-ins, multiple batches
Data <- BASiCS_Sim(Mu, Mu_spikes = NULL, Delta, 
                   Phi = NULL, S, Theta2, BatchInfo)

catavallejos/BASiCS documentation built on March 27, 2024, 12:49 a.m.