qtlhot (version 1.2.10)

filter.threshold: Summary of threshold results

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 = summary(hotperm(cross, max(s.quant), n.perm, alpha.levels, lod.thrs, verbose
    = verbose)),
  ww.thrs = summary(ww.perm(highobj, n.perm, lod.thrs, alpha.levels)),
  addcovar = NULL,
  intcovar = NULL,
  verbose = FALSE,
  ...
)

Value

List with items

NL.thrs

N.thrs

WW.thrs

NL

N.counts

WW.counts

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

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