arithscanperm: Arithmetic Operators for permutation results
In byandell/qtl: Tools for analyzing QTL experiments

Description Usage Arguments Details Value Author(s) Examples

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

1 2	perm1+perm2 perm1-perm2

perm1, perm2

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

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.

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

Karl W Broman, kbroman@biostat.wisc.edu

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)