splatPopParseEmpirical {splatter} | R Documentation

## splatPopParseEmpirical

### Description

Parse splatPop key information from empirical data provided.

### Usage

    splatPopParseEmpirical(
      vcf = vcf,
      gff = gff,
      eqtl = eqtl,
      means = means,
      params = params
    )

### Arguments

`vcf` | VariantAnnotation object containing genotypes of samples.
`gff` | Either NULL or a data.frame object containing a GFF/GTF file.
`eqtl` | Either NULL or if simulating population parameters directly from empirical data, a data.frame with empirical/desired eQTL results. To see required format, run 'mockEmpiricalSet()' and see eqtl output.
`means` | Either NULL or if simulating population parameters directly from empirical data, a Matrix of real gene means across a population, where each row is a gene and each column is an individual in the population. To see required format, run 'mockEmpiricalSet()' and see means output.
`params` | SplatPopParams object containing parameters for population scale simulations. See `SplatPopParams` for details.

### Details

NOTE: This function will cause some of the parameters in the splatPopParams object to be ignored, such as population level gene mean and variance and eQTL parameters.

This function will ignore a number of parameters defined in splatPopParams, instead pulling key information directly from provided VCF, GFF, gene means, and eQTL mapping result data provided.

### Value

A partial splatPop 'key'

[Package splatter version 1.18.2 Index]