R: Arithmetic operators for scanone and scantwo results

arithscan {qtl} | R Documentation

## Arithmetic operators for scanone and scantwo results

### Description

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

### Usage

    scan1+scan2
    scan1-scan2

### Arguments

`scan1, scan2` | Genome scan results on the same set of chromosomes and markers, as output by `scanone` or `scantwo`.

### Details

This is used to calculate the sum or difference of LOD scores of two genome scan results. It is particularly useful for calculating the LOD scores for QTL-by-covariate interactions (see the example, below). Note that the degrees of freedom are also added or subtracted.

### Value

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

### Author(s)

Karl W Broman, broman@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")

    # scan with additive but not the interactive covariate
    out.acovar <- scanone(fake.bc, addcovar=ac)

    # scan with interactive covariate
    out.icovar <- scanone(fake.bc, addcovar=ac, intcovar=ic)

    # plot the difference of with and without the interactive covariate
    #     This is a LOD score for a test of QTL x covariate interaction
    plot(out.icovar-out.acovar)

[Package qtl version 1.46-2 Index]