hotperm function

Conduct NL and N permutation tests

Conduct NL and N permutation tests.

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 class 'hotperm'
print(x, ...)
## S3 method for class 'hotperm'
summary(object, quant.levels, ...)
## S3 method for class 'hotperm'
quantile(x, probs, ..., lod.thr = NULL)
## S3 method for class '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

Author(s)

Elias Chaibub Neto and Brian S Yandell

Examples

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)
## End(Not run)

summary(hotperm1)