splatPopParseEmpirical: splatPopParseEmpirical

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

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'

Oshlack/splatter documentation built on Nov. 15, 2024, 7:25 p.m.