simpleEstimate: Estimate simple simulation parameters

Description Usage Arguments Details Value Examples

View source: R/simple-estimate.R

Description

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

Usage

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simpleEstimate(counts, params = newSimpleParams())

## S3 method for class 'SingleCellExperiment'
simpleEstimate(counts,
  params = newSimpleParams())

## S3 method for class 'matrix'
simpleEstimate(counts, params = newSimpleParams())

Arguments

counts

either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from.

params

SimpleParams object to store estimated values in.

Details

The nGenes and nCells parameters are taken from the size of the input data. The mean parameters are estimated by fitting a gamma distribution to the library size normalised mean expression level using fitdist. See SimpleParams for more details on the parameters.

Value

SimpleParams object containing the estimated parameters.

Examples

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# Load example data
library(scater)
data("sc_example_counts")

params <- simpleEstimate(sc_example_counts)
params

Oshlack/splatter documentation built on Oct. 5, 2018, 11:14 a.m.