lun2Estimate: Estimate Lun2 simulation parameters

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

Estimate Lun2 simulation parameters

Description

Estimate simulation parameters for the Lun2 simulation from a real dataset.

Usage

lun2Estimate(
  counts,
  plates,
  params = newLun2Params(),
  min.size = 200,
  verbose = TRUE,
  BPPARAM = SerialParam()
)

## S3 method for class 'SingleCellExperiment'
lun2Estimate(
  counts,
  plates,
  params = newLun2Params(),
  min.size = 200,
  verbose = TRUE,
  BPPARAM = SerialParam()
)

## S3 method for class 'matrix'
lun2Estimate(
  counts,
  plates,
  params = newLun2Params(),
  min.size = 200,
  verbose = TRUE,
  BPPARAM = SerialParam()
)

Arguments

counts	either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from.
plates	integer vector giving the plate that each cell originated from.
params	Lun2Params object to store estimated values in.
min.size	minimum size of clusters when identifying group of cells in the data.
verbose	logical. Whether to show progress messages.
BPPARAM	A BiocParallelParam instance giving the parallel back-end to be used. Default is SerialParam which uses a single core.

Details

See Lun2Params for more details on the parameters.

Value

LunParams object containing the estimated parameters.

Examples

# Load example data
library(scuttle)
set.seed(1)
sce <- mockSCE()

plates <- as.numeric(factor(colData(sce)$Mutation_Status))
params <- lun2Estimate(sce, plates, min.size = 20)
params

Oshlack/splatter documentation built on May 8, 2024, 5:33 a.m.