Once scan1snps() was written, we simplified the user guide, pulling out all the discussion of the internal details, as they're mostly not necessary anymore. But it would be good to add a tutorial that fully explains them:
- connecting to a snp database to get snp information
- calculating strain distribution patterns if not present
- indexing the SNPs
- using
genoprob_to_snpprob()
- calling
scan1() with those results