qtl.simulate: Simulate a QTL in the DO

Description

Using a set of real DO genomes, simulate a QTL with a given minor allele frequency (MAFALSE), sample size and effect size.

Usage

qtl.simulate(probs, snps, K, sample.size = dim(probs)[[1]], effect.size = 1,  maf = 4, num.poly = 18, num.sims = 1000)

Arguments

probs

Numeric three dimensional array, containing the founder haplotype contributions or genotype probabilities. The sample IDs, founder letter codes and markers IDs must be in dimnames.

snps

Data.frame containing 4 columns with marker location information. SNP ID, chr, Mb, cM in columns 1 through 4, respectively.

Numeric matrix, containing the additive kinship matrix. The samples IDs must be in rownames and colnames.

sample.size

Numeric vector sample sizes. Must be less than or equal to the number of samples in probs.

effect.size

Numeric vector containing the effect sizes as the number of standard deviations from the phenotype mean.

maf

Numeric value containing the minor allele frequecy as the number of founders. FALSEor DO, the value must be between 1 and 4.

num.poly

Numeric value containing the number of autosomes on which to simulate a polygenic background.

num.sims

Numeric value containing the number of simulations to run.

Value

Writes pheno and qtl lists to an R binary file.

Details

This function will simulate a phenotype with a QTL. It will output a phenotype vector with sample IDs and a data.frame called qtl describing the simulated loci.

Examples

Run this code

  ## Not run:  qtl.simulate(probs, snps, K, sample.size = dim(probs)[[1]], 
#   effect.size = 1, maf = 4, num.poly = 18, num.sims = 1000) ## End(Not run)