R: Estimate scDD simulation parameters

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 1.12.0 Index]