splatPopEstimate {splatter} | R Documentation

## 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(scater)

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

[Package splatter version 1.14.1 Index]