zinbEstimate {splatter} | R Documentation

## Estimate ZINB-WaVE simulation parameters

### Description

Estimate simulation parameters for the ZINB-WaVE simulation from a real dataset.

### Usage

    zinbEstimate(counts, design.samples = NULL, design.genes = NULL,
      common.disp = TRUE, iter.init = 2, iter.opt = 25, stop.opt = 1e-04,
      params = newZINBParams(), verbose = TRUE, BPPARAM = SerialParam(), ...)

    ## S3 method for class 'SingleCellExperiment'
    zinbEstimate(counts, design.samples = NULL,
      design.genes = NULL, common.disp = TRUE, iter.init = 2, iter.opt = 25,
      stop.opt = 1e-04, params = newZINBParams(), verbose = TRUE,
      BPPARAM = SerialParam(), ...)

    ## S3 method for class 'matrix'
    zinbEstimate(counts, design.samples = NULL,
      design.genes = NULL, common.disp = TRUE, iter.init = 2, iter.opt = 25,
      stop.opt = 1e-04, params = newZINBParams(), verbose = TRUE,
      BPPARAM = SerialParam(), ...)

### Arguments

`counts` | either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from.
`design.samples` | design matrix of sample-level covariates.
`design.genes` | design matrix of gene-level covariates.
`common.disp` | logical. Whether or not a single dispersion for all features is estimated.
`iter.init` | number of iterations to use for initalization.
`iter.opt` | number of iterations to use for optimization.
`stop.opt` | stopping criterion for optimization.
`params` | ZINBParams object to store estimated values in.
`verbose` | logical. Whether to print progress messages.
`BPPARAM` | A `BiocParallelParam` instance giving the parallel back-end to be used. Default is `SerialParam` which uses a single core.
`...` | additional arguments passes to `zinbFit`.

### Details

The function is a wrapper around `zinbFit` that takes the fitted model and inserts it into a `ZINBParams` object. See `ZINBParams` for more details on the parameters and `zinbFit` for details of the estimation procedure.

### Value

ZINBParams object containing the estimated parameters.

### Examples

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

    params <- zinbEstimate(sc_example_counts)
    params

    ## End(Not run)

[Package splatter version 1.4.3 Index]