zinbEstimate: Estimate ZINB-WaVE simulation parameters

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

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(scuttle)
    set.seed(1)
    sce <- mockSCE(ncells = 20, ngenes = 100)

    params <- zinbEstimate(sce)
    params
}

Oshlack/splatter documentation built on Dec. 10, 2024, 3:48 p.m.