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 initialization.
`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

    if (requireNamespace("zinbwave", quietly = TRUE)) {
        library(scater)
        set.seed(1)
        sce <- mockSCE(ncells = 20, ngenes = 100)

        params <- zinbEstimate(sce)
        params
    }

[Package splatter version 1.14.1 Index]