lun2Estimate: Estimate Lun2 simulation parameters

Description Usage Arguments Details Value Examples

View source: R/lun2-estimate.R

Description

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

Usage

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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

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## 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)

Oshlack/splatter documentation built on April 21, 2018, 3:18 p.m.