qtl.simulate: Simulate a QTL in the DO

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

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.
K	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.

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.

Value

Writes pheno and qtl lists to an R binary file.

Author(s)

Daniel Gatti

See Also

scanone

Examples

  ## 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)

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.