qtlhot (version 1.2.10)

sim.hotspot: Wrapper routine for simulations.

Description

Simulate `nSim` realizations of cross object with `n.pheno` phenotypes with correlation `latent.eff`. All simulations use the same genotypes in the `cross` object.

Usage

sim.hotspot(
  nSim,
  cross,
  n.pheno,
  latent.eff,
  res.var = 1,
  n.quant,
  n.perm,
  alpha.levels,
  lod.thrs,
  drop.lod = 1.5,
  verbose = FALSE
)

Value

`sim.null.cross` simulates an object of class `cross`. `sim.null.pheno.data` simulates a data frame of phenotypes. `sim.hotspot` uses these other routines to simulate a hotspot, returning an list object.

Arguments

nSim

Number of simulated sets of phenotypes to create. See details.

cross

Object of class `cross`. See read.cross.

n.pheno

Number of traits, or phenotypes, to simulate for cross object.

latent.eff

Strength of latent effect, which is included in all traits. See sim.null.cross.

res.var

Residual variance for traits. Should not affect results.

n.quant

maximum size of hotspots examined; ideally large enough to exceed the largest Breitling alpha critical value.

n.perm

Number of permutations to perform per realization. Good idea to do 1000, but this takes time.

alpha.levels

Vector of significance levels.

lod.thrs

Vector of LOD thresholds, typically single-trait permutation thresholds for various significance levels.

drop.lod

Drop in LOD score examined. LODs below this drop from the maximum for a chromosome will not be scored.

verbose

verbose output if TRUE

Author

Elias Chaibub Neto and Brian S. Yandell

See Also

sim.null.cross, read.cross.

Examples

ncross1 <- sim.null.cross(chr.len = rep(100, 4),
                          n.mar = 51,
                          n.ind = 100,
                          type = "bc",
                          n.phe = 1000,
                          latent.eff = 3,
                          res.var = 1,
                          init.seed = 123457)
cross1 <- include.hotspots(cross = ncross1,
                           hchr = c(2, 3, 4),
                           hpos = c(25, 75, 50),
                           hsize = c(100, 50, 20),
                           Q.eff = 2,
                           latent.eff = 3,
                           lod.range.1 = c(2.5, 2.5),
                           lod.range.2 = c(5, 8),
                           lod.range.3 = c(10, 15),
                           res.var = 1,
                           n.phe = 1000,
                           init.seed = 12345)