permutation exercise

[smcclatchy]

new_order <- sample(rownames(iron$pheno))
pheno_perm <- iron$pheno
rownames(pheno_perm) <- new_order
xcovar_perm <- Xcovar
rownames(xcovar_perm) <- new_order
p <- scan1(genoprobs = pr, pheno = pheno_perm, Xcovar = xcovar_perm)
plot(p, map)
head(new_order)

regular scan has max lod ~ 7

new permutation has max lod ~ 2

scrambled all the data so that phenotypes are no longer connected to the sample or mouse

what is max lod by chance?

paste your max lod into etherpad
load all max lods into a vector
create a histogram of max lods
do 1000 perms as in the lesson
plot the max lod in a histogram
max a hist of operm[,1]
now on your own, hist of operm[,2]
draw abline for 0.2 or 0.05 threshold for liver or spleen onto histogram
abline(v = 3.36, col = "red")
now on your own, do the same for spleen, for 0.2 , etc. use blue, gray etc.