scDDEstimate: Estimate scDD simulation parameters

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

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(scuttle)
    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
}

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