% Generated by roxygen2: do not edit by hand % Please edit documentation in R/splat-eqtl.R \name{splateQTL} \alias{splateQTL} \title{Splat-eQTL} \usage{ splateQTL( params = newSplatParams(), gff = ex_gff, snps = ex_snps, eqtlES_shape = 2.740558, eqtlES_rate = 6.441281, esnp.n = 100, eqtl.dist = 1e+06, eqtl.maf = 0.1, eqtl.mafd = 0.01, eqtl.save = TRUE, ... ) } \arguments{ \item{params}{SplatParams object containing parameters for the simulation. See \code{\link{SplatParams}} for details.} \item{gff}{Dataframe containing the genes to include in GFF/GTF format.} \item{snps}{Dataframe containing real/simulated genotype data in .vcf format. Where each column is a sample and each row is a SNP.} \item{eqtlES_shape}{Effect Size shape parameter (default estimated from GTEx thyroid cis-eQTL data)} \item{eqtlES_rate}{Effect Size rate parameter (default estimated from GTEx thyroid cis-eQTL data)} \item{esnp.n}{Number of eSNP-eQTL associations to include} \item{eqtl.dist}{Distance between eSNP and eGene (TSS).} \item{eqtl.maf}{Desired Minor Allele Frequency (MAF) of eSNPs to include} \item{eqtl.mafd}{Maximum variation from eqtl.maf to include as eSNP} \item{eqtl.save}{logical. Whether to save eQTL key and mean matrix.} \item{...}{any additional parameter settings to override what is provided in \code{params}.} } \value{ GeneMeansPop Matrix containing the simulated mean gene expression value for each gene (row) and each sample in the population (column). intermediate values. } \description{ Simulate mean gene counts for a population of samples, such that a defined number of associations (cis-eQTL) between markers (eSNPs) and genes (eGenes) exist. } \details{ Parameters can be set in a variety of ways. If no parameters are provided the default parameters are used. Any parameters in \code{params} can be overridden by supplying additional arguments through a call to \code{\link{setParams}}. This design allows the user flexibility in how they supply parameters and allows small adjustments without creating a new \code{SplatParams} object. See examples for a demonstration of how this can be used. The eQTL Gene Mean simulation involves the following steps: \enumerate{ \item Load and format gene (GFF/GTF) and SNP (genotype) data. \item Select eGenes-eSNPs pairs and assign effect sizes. \item Generate normalized gene mean expression matrix for the population. \item Set a gene mean expression value (not normalized) for each gene. \item Generate a gene mean expression matrix for the population. \item (optional) Save eQTL key (pairs) } } \examples{ # Load example data library(scater) set.seed(1) sce <- mockSCE() params <- splatEstimate(sce) data(ex_gff) data(ex_snps) pop.gMeans <- splateQTL(params) } \seealso{ \code{\link{splateQTLgenes}}, \code{\link{splateQTLsnps}}, \code{\link{splateQTLpairs}}, \code{\link{splateQTLnormMeansMatrix}}, \code{\link{splateQTLGeneMeans}}, \code{\link{splateQTLMeansMatrix}} }