Post date: Dec 10, 2015 7:44:10 PM
Posterior distributions for the scale parameter and ancestry frequencies were summarized with estpost using the wrapper script estParms.pl. The raw hdf5 output from estpost was then moved to /labs/evolution/projects/popanc_sims/mcmc/mig/. The parameter estimates are in /labs/evolution/projects/popanc_sims/analysis/parms/.
Prior to making plots and calculating further summaries, I analyzed the simulated data with the linkage model in structure and obtained true ancestry frequencies.
structure analysis:
1. Infiles for structure were created from the geno* files (for popanc) using the script mkStructureIn.pl: perl ../../structure/mkStructIn.pl genoAdmxF_r*
2. Jobs were submitted to run structure using the script (see infiles subdirectory in the structure directory). Here is an example job:
cd /local/scratch/
sleep 5
structure -i /labs/evolution/projects/popanc_sims/structure/infiles/genostructF_r9gen_demog_mig0.05.txt -m /labs/evolution/projects/popanc_sims/structure//mainparams -e /labs/evolution/projects/popanc_sims/structure//extraparams -o out_struct_r9gen_demog_mig0.05Chain1
scp out_struct_r9gen_demog_mig0.05Chain1* /labs/evolution/projects/popanc_sims/structure/
3. Posteriors summarized
true ancestry:
True ancestry frequencies were calculated with the script calcTrueAnc.pl in /labs/evolution/projects/popanc_sims/sims/, as follows:
perl calcTrueAnc.pl gen_demog_mig0.05.txt
perl calcTrueAnc.pl gen_demog_mig0.005.txt
Ancestry frequencies are in the trueAnc* files in /labs/evolution/projects/popanc_sims/analysis/true/.
Plots and summaries:
1. Updated the local ancestry variance plot (Fig. 2) with the new migration results. See plotLancVar.R and ancvar.eps.
2. Generated plot of example ancestry frequencies (true and estimated) for a single low and high migration replicate (analogosu to Fig. 4, this will be Fig. 7).