qtl.simulate {DOQTL} | R Documentation

## 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)

[Package DOQTL version 1.16.2 Index]