# arithscanperm: Arithmetic Operators for permutation results In qtl: Tools for Analyzing QTL Experiments

## Description

Add or subtract LOD scores in permutation results from `scanone` or `scantwo`.

## Usage

 ```1 2``` ```perm1+perm2 perm1-perm2 ```

## Arguments

 `perm1, perm2` Permutation results from `scanone` or `scantwo`, on the same set of chromosomes and markers.

## Details

This is used to calculate the sum or difference of LOD scores of two sets of permutation results from `scanone` or `scantwo`. One must be careful to ensure that the permutations are perfectly linked, which will require the use of `set.seed`.

## Value

The same data structure as the input objects, with LOD scores added or subtracted.

## Author(s)

Karl W Broman, [email protected]

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30``` ```data(fake.bc) fake.bc <- calc.genoprob(fake.bc, step=2.5) # covariates ac <- pull.pheno(fake.bc, c("sex","age")) ic <- pull.pheno(fake.bc, "sex") # set seed theseed <- round(runif(1, 1, 10^8)) set.seed(theseed) # permutations with additive but not the interactive covariate ## Not run: operm.acovar <- scanone(fake.bc, addcovar=ac, n.perm=1000) # re-set the seed set.seed(theseed) # permutations with interactive covariate ## Not run: operm.icovar <- scanone(fake.bc, addcovar=ac, intcovar=ic, n.perm=1000) ## End(Not run) # permutation results for the QTL x covariate interaction operm.gxc <- operm.icovar - operm.acovar # LOD thresholds summary(operm.gxc) ```

qtl documentation built on Feb. 20, 2018, 1 a.m.