lun2Estimate: Estimate Lun2 simulation parameters

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

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

## Not run: 
# Load example data
library(scater)
data("sc_example_counts")
data("sc_example_cell_info")

plates <- factor(sc_example_cell_info$Mutation_Status)
params <- lun2Estimate(sc_example_counts, plates, min.size = 20)
params

## End(Not run)

Granoia/splatter-mod documentation built on May 28, 2019, 12:31 a.m.