### Checked the allele frequency for 58 shared SNPs between east and west. Repeated the same randomizations which I used for the experimental correlations effect signs. #####
The code (filename = effSigns_quantiles_randomization_top.R) is saved in the following directory:
/uufs/chpc.utah.edu/common/home/u6007910/projects/lmelissa_hostAdaptation/ExperimentalComparison/march17_finalAnalysis
File relevant for this analysis are:
melissaAll_allelefreqs.txt, melissaEast_allelefreqs.txt, melissaWest_allelefreqs.txt = files with raw allele frequencies for these population sets
top58snps_scafPosBayesfactors = details of 58 shared SNPs
For standardized allele frequencies
Randomization1
pvalue = 0.222
Xfold = 1.043201
Randomization2
pvalue = 0.257
xfold = 1.06114
For raw allele frequencies
Randomization1
pvalue = 0.218
Xfold = 1.053871
Randomization2
pvalue = 0.046
xfold = 1.209577