qtlhot (version 1.0.4)

hotperm: Conduct NL and N permutation tests

Description

Conduct NL and N permutation tests.

Usage

hotperm(cross, n.quant, n.perm, lod.thrs, alpha.levels, drop.lod = 1.5,
  window = NULL, verbose = FALSE, init.seed = 0,
  addcovar = NULL, intcovar = NULL, …)
data(hotperm1)
# S3 method for hotperm
print(x, …)
# S3 method for hotperm
summary(object, quant.levels, …)
# S3 method for hotperm
quantile(x, probs, …, lod.thr = NULL)
# S3 method for summary.hotperm
print(x, …)

Arguments

cross

object of class cross

n.quant

maximum of s.quant

n.perm

number of permutations

lod.thrs

vector of LOD thresholds

alpha.levels

vector of significance levels

quant.levels

quantile levels, as number of traits, to show in summary; default is 1, 2, 5, 10, … up to maximum recorded

drop.lod

LOD drop amount for support intervals

window

window size for smoothed hotspot size

verbose

verbose output if TRUE

init.seed

initial seed for pseudo-random number generation

x,object

object of class hotperm or summary.hotperm

probs

probability levels for quantiles (1-probs if all > 0.5); default is alpha.levels

lod.thr

restrict to values above this if not NULL

addcovar

additive covariates as vector or matrix; see scanone

intcovar

interactive covariates as vector or matrix; see scanone

…

arguments passed along to scanone

Examples

# NOT RUN {
example(include.hotspots)
set.seed(123)
pt <- scanone(ncross1, method = "hk", n.perm = 1000)
alphas <- seq(0.01, 0.10, by=0.01)
lod.thrs <- summary(pt, alphas)
# }
# NOT RUN {
## This takes awhile, so we save the object.
set.seed(12345)
hotperm1 <- hotperm(cross = cross1,
                    n.quant = 300,
                    n.perm = 100,
                    lod.thrs = lod.thrs,
                    alpha.levels = alphas,
                    drop.lod = 1.5,
                    verbose = FALSE)
save(hotperm1, file = "hotperm1.RData", compress = TRUE)
# }
# NOT RUN {
summary(hotperm1)
# }