Add or subtract LOD scores in permutation results from
Permutation results from
This is used to calculate the sum or difference of LOD scores of two
sets of permutation results from
scantwo. One must be careful to ensure that the
permutations are perfectly linked, which
will require the use of
The same data structure as the input objects, with LOD scores added or subtracted.
Karl W Broman, email@example.com
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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)
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