splatPopParseEmpirical

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.

Value

A partial splatPop `key`

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.