Arithmetic operators for scanone and scantwo results
scan1+scan2 scan1-scan2
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.
The same type of data structure as the input objects, with LOD scores added or subtracted.
Karl W Broman, broman@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")
# 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.