splatPopEstimate: Estimate population/eQTL simulation parameters

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

Estimate population/eQTL simulation parameters

Description

Estimate simulation parameters for the eQTL population simulation from real data. See the individual estimation functions for more details on how this is done.

Usage

splatPopEstimate(
  counts = NULL,
  means = NULL,
  eqtl = NULL,
  params = newSplatPopParams()
)

Arguments

counts	either a counts matrix or a SingleCellExperiment object containing count data to estimate parameters from.
means	Matrix of real gene means across a population, where each row is a gene and each column is an individual in the population.
eqtl	data.frame with all or top eQTL pairs from a real eQTL analysis. Must include columns: 'gene_id', 'pval_nominal', and 'slope'.
params	SplatPopParams object containing parameters for the simulation of the mean expression levels for the population. See SplatPopParams for details.

Value

SplatPopParams object containing the estimated parameters.

See Also

splatPopEstimateEffectSize, splatPopEstimateMeanCV

Examples

if (requireNamespace("VariantAnnotation", quietly = TRUE) &&
    requireNamespace("preprocessCore", quietly = TRUE)) {
    # Load example data
    library(scuttle)

    sce <- mockSCE()
    params <- splatPopEstimate(sce)
}

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