filter.threshold function

Summary of threshold results

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, ...)

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

Returns

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