Description Usage Arguments Details Value Author(s) Examples
Add or subtract LOD scores in permutation results from
scanone
or scantwo
.
1 2  perm1+perm2
perm1perm2

perm1, perm2 
Permutation results from

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, [email protected]
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)
# reset 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)

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