hotperm: Conduct NL and N permutation tests

In byandell/qtlhot: Inference for QTL Hotspots

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 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)

byandell/qtlhot documentation built on March 7, 2020, 3:25 p.m.