One-locus summary
Read more about these tools (and see examples of input files) in the usage overview.
Provides numeric frequency estimate results and a graphic representation of the relevant EM-based frequency estimates, assesment of Hardy-Weinberg equilibrium (nested likelihood ratio test) and selective neutrality (adapted from the Slatkin-Ewens-Watterson neutrality test).
Filenames of type Lab_Region_Population_Locus.unif are expected (e.g. AHPD-collection_SE-EUR_Slovenians_A.unif) and input must be a valid UNIFORMAT file with .unif extension.
When I ran the one locus analysis, The following error occurred “Ouch. An error occured: user directory not writable or missing”
What does it mean?
with regards
Vani
Dear Vani,
I believe you already received a reply concerning some malfunction that should be solved by now.
As I had a look at your inputs, I just take the occasion to suggest that for now (hopefully until May, when the new version will be available) you should use one file for each locus and not one with all loci (I agree it is not very practical, and that’s why it will change).
Thanks for using gene[rate].
Kind regards,
Dear Nunes,
If I use one file for each locus, how do I calculate LD for two locus haplotypes and select the haplotypes which are significant.
with regards
Vani
While waiting for the new version that unifies one and two (and more) loci summaries, the best option is to create files for each locus and for each pair of loci (usually consecutive), and then submit one locus files to one locus summary and the two locus files the the two-locus tool.