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 1.6.5 Index]