Description Usage Arguments Author(s) Examples
Conduct NL and N permutation tests.
1 2 3 4 5 6 7 8 9 10 11 12 | 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, ...)
|
cross |
object of class |
n.quant |
maximum of |
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 |
init.seed |
initial seed for pseudo-random number generation |
x,object |
object of class |
probs |
probability levels for quantiles ( |
lod.thr |
restrict to values above this if not |
addcovar |
additive covariates as vector or matrix; see |
intcovar |
interactive covariates as vector or matrix; see |
... |
arguments passed along to |
Elias Chaibub Neto and Brian S Yandell
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | 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)
|
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