scDDEstimate {splatter} | R Documentation

## Estimate scDD simulation parameters

### Description

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

### Usage

    scDDEstimate(
      counts,
      params = newSCDDParams(),
      verbose = TRUE,
      BPPARAM = SerialParam(),
      ...
    )

    ## S3 method for class 'matrix'
    scDDEstimate(
      counts,
      params = newSCDDParams(),
      verbose = TRUE,
      BPPARAM = SerialParam(),
      conditions,
      ...
    )

    ## S3 method for class 'SingleCellExperiment'
    scDDEstimate(
      counts,
      params = newSCDDParams(),
      verbose = TRUE,
      BPPARAM = SerialParam(),
      condition = "condition",
      ...
    )

    ## Default S3 method:
    scDDEstimate(
      counts,
      params = newSCDDParams(),
      verbose = TRUE,
      BPPARAM = SerialParam(),
      condition,
      ...
    )

### Arguments

`counts` | either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from.
`params` | SCDDParams object to store estimated values in.
`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.
`...` | further arguments passed to or from other methods.
`conditions` | Vector giving the condition that each cell belongs to. Conditions can be 1 or 2.
`condition` | String giving the column that represents biological group of interest.

### Details

This function applies `preprocess` to the counts then uses `scDD` to estimate the numbers of each gene type to simulate. The output is then converted to a SCDDParams object. See `preprocess` and `scDD` for details.

### Value

SCDDParams object containing the estimated parameters.

### Examples

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

        colData(sce)$condition <- sample(1:2, ncol(sce), replace = TRUE)
        params <- scDDEstimate(sce, condition = "condition")
        params
    }

[Package splatter version 1.18.2 Index]