filter.threshold: Summary of threshold results

In byandell/qtlhot: Inference for QTL Hotspots

Description

Summary of threshold results.

Usage

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, ...)

Arguments

cross	object of class cross; see read.cross
pheno.col	phenotype columns used for filtering thresholds
latent.eff	ratio of latent effect SD to residual SD
res.var	residual variance (=SD^2)
lod.thrs	LOD threshold values for range of significance (alpha) levels
drop.lod	LOD drop from max LOD to keep in analysis
s.quant	vector of 1:Nmax with Nmax the maximum hotspot size to be considered
n.perm	number of permutations
alpha.levels	range of significance levels; same length as lod.thrs
qh.thrs	Results of call to hotperm
ww.thrs	Results of call to ww.perm
addcovar	additive covariates as vector or matrix; see scanone
intcovar	interactive covariates as vector or matrix; see scanone
verbose	verbose output if TRUE
...	arguments passed along to scanone

Value

List with items

NL.thrs
N.thrs
WW.thrs
NL
N.counts
WW.counts

References

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.

See Also

hotperm, ww.perm, scanone

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