cd DIRECTORY_WITH_DATA

## mac:
cp ../osx/* . #copy programs to current directory
./selscan --ihs --map CEU.chr2.map --hap CEU.chr2.ihshap --out CEU.chr2
./norm --ihs --files CEU.chr2.ihs.out bg.ihs.out

## linux:
cp ../linux/* . #copy programs to current directory
./selscan --ihs --map CEU.chr2.map --hap CEU.chr2.ihshap --out CEU.chr2
./norm --ihs --files CEU.chr2.ihs.out bg.ihs.out

## windows:
cp ..\win\* . #copy programs to current directory
selscan.exe --ihs --map CEU.chr2.map --hap CEU.chr2.ihshap --out CEU.chr2
norm.exe --ihs --files CEU.chr2.ihs.out bg.ihs.out


## R commands

setwd("DIRECTORY_WITH_DATA")

CEU=read.table("CEU.chr2.ihs.out.100bins.norm")

plot(CEU[,2], CEU[,7]) #normalized iHS values

plot(CEU[,2], abs(CEU[,7])) # absolute value of normalized iHS values

## let's smooth this data with loess!!
SP=0.2 #this is the span, a parameter you can change (higher = more smoothing)
CEU.x=CEU[,2]; #the x-coordinates in Mb
y=abs(CEU[,7]) #iHS is actually the absolute value
CEU.loess=loess(y~CEU.x,span=SP,data.frame(x=CEU.x,y=y)); #step 1
CEU.predict=predict(CEU.loess,data.frame(x=CEU.x)); #step 2

plot(CEU[,2], abs(CEU[,7])) # absolute value of normalized iHS values
lines(CEU.x, CEU.predict, lwd=2, col='blue')