R: Arithmetic Operators for permutation results

arithscanperm {qtl} | R Documentation

## Arithmetic Operators for permutation results

### Description

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

### Usage

    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, kbroman@biostat.wisc.edu

### Examples

    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)

[Package qtl version 1.41-6 Index]