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

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

    conditions <- sample(1:2, ncol(sc_example_counts), replace = TRUE)
    params <- scDDEstimate(sc_example_counts, conditions = conditions)
    params

    ## End(Not run)

[Package splatter version 1.6.1 Index]