step.fitqtl {qtlbim}R Documentation

Stepwise backward elimination and anova comparison.

Description

These functions mimic step and anova but have reduced functionality. They are not truly methods, but can help study qtl model fits.

Usage

step.fitqtl(cross, qtl, pheno.col = 1, arch, cutoff = 0.05,
  trace = 1, steps = 100)
## S3 method for class 'step.fitqtl':
anova(object, object2, ...)

Arguments

cross Object of class cross.
qtl Object of class qtl, as output of makeqtl.
pheno.col Column of phenotype (numeric).
arch Object of class qb.arch from qb.arch.
cutoff Significance cutoff for dropping terms.
trace If positive, information is printed during the run. Values 1, 2, 3 give gradually more detailed information.
steps Maximum number of steps to be considered.
object Object of class step.fitqtl from step.fitqtl.
object2 Object of class step.fitqtl from step.fitqtl.
... Currently not used.

Details

step.fitqtl is analogous to step applied to analysis with fitqtl. anova.step.fitqtl is an S3 method for anova. anova.step.fitqtl with one argument calls summary.fitqtl; with two arguments it attempts to conduct a general F comparison of anova fits.

Value

step.fitqtl returns an object of class step.fitqtl with

fit Object of class fitqtl.
arch Object of class qb.arch.

Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

References

http://www.qtlbim.org

See Also

qb.arch, fitqtl, summary.fitqtl, makeqtl

Examples


cross <- sim.geno(cross, n.draws = 8, step = 2, error = 0.01)
qtl <- makeqtl(cross, chr = c(1,1,2,3), pos = c(15,45,12,15))
cross.step <- step.fitqtl(cross, qtl, pheno.col = 3, arch = cross.arch)
anova(cross.step)
cross.step$arch

[Package qtlbim version 1.9.3 Index]