Human chr15 SLC24A5 pigmentation gene

Coming back to being human, we look at chr15 DAF's. The most prominent feature is the short_arm (information not available). Having come across the database of recent positive selection across human populations (dbPSHP), i was hoping to see a clear signal of DAF near the SLC24A5 gene. It does not seem to be one of the more prominent DAF peaks. Infact, adding the SV2B gene onto the plot does not bring it near any of the prominent DAF peaks. Will have to see how many of my DAF peaks actually match up those in the dbPSHP.

The correlation coefficient of 0.3277578 between the mean derived allele frequency and Number of CNV's is line with the results from other chromosomes.

The code is not different from before:

 chr <- "chr15";    
 jpeg(paste("DAF.",chr,".jpeg",sep=""),width=1420)    
 par(mfrow=c(2,1))    
 read.table(file=paste("h.",chr,".mean.bed",sep=""),header=F,stringsAsFactors=F)->M    
 plot(as.numeric(M$V2),as.numeric(M$V4),xlab="Position along chromosome",ylab="Mean derived allele Frequency",main=chr)    
 lines(c(10000,17000000),c(0.2,0.2),col="red",lwd=5)    
 text(10000, 0.25,labels="short_arm",col="red")    
 lines(c(101981189,101991189),c(0.3,0.3),col="blue",lwd=5)    
 text(101981189, 0.35,labels="Telomere",col="blue")    
 lines(c(0,10000),c(0.3,0.3),col="blue",lwd=5)    
 text(0, 0.35,labels="Telomere",col="blue")    
 lines(c(48413169,48434589),c(0.25,0.25),col="brown",lwd=5)    
 text(48413169, 0.3,labels="SLC24A5 gene",col="brown")    
 lines(c(91643182,91844539),c(0.25,0.25),col="brown",lwd=5)    
 text(91643182, 0.3,labels="SV2B gene",col="brown")    
 read.table(file=paste("h.",chr,".countdgv.bed",sep=""),header=FALSE)->C    
 plot(C$V2,C$V4,xlab="Position along chromosome",ylab="Count of known structural variants",main=chr)    
 cor.test(as.numeric(M$V4),C$V4,method="spearman")    
 dev.off()