Summary of threshold results.
filter.threshold(cross, pheno.col, latent.eff, res.var, lod.thrs, drop.lod = 1.5,
s.quant, n.perm, alpha.levels, qh.thrs, ww.thrs, addcovar = NULL,
intcovar = NULL, verbose = FALSE, …)object of class cross; see read.cross
phenotype columns used for filtering thresholds
ratio of latent effect SD to residual SD
residual variance (=SD^2)
LOD threshold values for range of significance (alpha) levels
LOD drop from max LOD to keep in analysis
vector of 1:Nmax with Nmax the maximum hotspot
size to be considered
number of permutations
range of significance levels; same length as lod.thrs
Results of call to hotperm
Results of call to ww.perm
additive covariates as vector or matrix; see scanone
interactive covariates as vector or matrix; see scanone
verbose output if TRUE
arguments passed along to scanone
List with items
Manichaikul A, Dupuis J, Sen S, Broman KW (2006) Poor performance of bootstrap confidence intervals for the location of a quantitative trait locus. Genetics 174: 481-489.