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cooplab · Apr 18, 2013 · 89541d2 · 89541d2
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diff --git a/Figs/ simple_diploid_trajs.eps b/Figs/ simple_diploid_trajs.eps
diff --git a/Figs/CEU_YRI_separately_HWE-eps-converted-to.pdf b/Figs/CEU_YRI_separately_HWE-eps-converted-to.pdf
diff --git a/Figs/CEU_YRI_separately_HWE.eps b/Figs/CEU_YRI_separately_HWE.eps
diff --git a/Figs/CEU_YRI_separately_HWE.pdf b/Figs/CEU_YRI_separately_HWE.pdf
diff --git a/Figs/CEU_YRI_together_HWE-eps-converted-to.pdf b/Figs/CEU_YRI_together_HWE-eps-converted-to.pdf
diff --git a/Figs/CEU_YRI_together_HWE.eps b/Figs/CEU_YRI_together_HWE.eps
diff --git a/Figs/Genomewide_HH-eps-converted-to.pdf b/Figs/Genomewide_HH-eps-converted-to.pdf
diff --git a/Figs/Genomewide_HH.eps b/Figs/Genomewide_HH.eps
diff --git a/Figs/HH_diagram.pptx b/Figs/HH_diagram.pptx
diff --git a/Figs/HH_diagram.ps b/Figs/HH_diagram.ps
diff --git a/Figs/HWE_CEU.pdf b/Figs/HWE_CEU.pdf
diff --git a/Figs/QT1-eps-converted-to.pdf b/Figs/QT1-eps-converted-to.pdf
diff --git a/Figs/QT1.eps b/Figs/QT1.eps
diff --git a/Figs/QT2-eps-converted-to.pdf b/Figs/QT2-eps-converted-to.pdf
diff --git a/Figs/QT2.eps b/Figs/QT2.eps
diff --git a/Figs/QT3-eps-converted-to.pdf b/Figs/QT3-eps-converted-to.pdf
diff --git a/Figs/QT3.eps b/Figs/QT3.eps
diff --git a/Figs/equilib_cline-eps-converted-to.pdf b/Figs/equilib_cline-eps-converted-to.pdf
diff --git a/Figs/equilib_cline.eps b/Figs/equilib_cline.eps
diff --git a/Figs/hitchhiking_reduction-eps-converted-to.pdf b/Figs/hitchhiking_reduction-eps-converted-to.pdf
diff --git a/Figs/hitchhiking_reduction.eps b/Figs/hitchhiking_reduction.eps
diff --git a/Figs/simple_diploid_trajs-eps-converted-to.pdf b/Figs/simple_diploid_trajs-eps-converted-to.pdf
diff --git a/Figs/simple_diploid_trajs.eps b/Figs/simple_diploid_trajs.eps
diff --git a/Rcode/Genomewide_HH.R b/Rcode/Genomewide_HH.R
@@ -0,0 +1,11 @@
+  shapiro.data=read.table("~/Dropbox/Courses/PBGG_Core/Popgen_teaching_Notes/R code/shap_dat.txt")
+  rec=  shapiro.data$V3
+   pi=  shapiro.data$V4*100
+ plot(rec, pi, xlab="rec rate (cM/Mb)", ylab="Syn diversity (%)",cex.axis=1.4,cex.lab=1.5)
+ true.rec<-rec/10^8;
+ nls(pi~neutral.pi*true.rec/(true.rec+alpha),start=list(neutral.pi=2,alpha=1e-9))
+ lines(rec,2.75*true.rec/(true.rec+7.3e-9),col="red",lwd=3)
+
+fig.direct="~/Dropbox/Courses/PBGG_Core/Popgen_teaching_Notes/Figs/"
+
+dev.copy2eps(file=paste(fig.direct,"Genomewide_HH.eps",sep=""))
diff --git a/Rcode/HWE_exercise.zip b/Rcode/HWE_exercise.zip
diff --git a/Rcode/HWE_exercise/CEU_10000.hw.gz b/Rcode/HWE_exercise/CEU_10000.hw.gz
diff --git a/Rcode/HWE_exercise/CEU_YRI_10000.hw.gz b/Rcode/HWE_exercise/CEU_YRI_10000.hw.gz