In [1]:

    

HOME="/Users/haocheng/Github/SSBR.jl"
cd(HOME)
include("src/SSBR.jl")


    

In [3]:

    

Pkg.clone("https://github.com/reworkhow/SSBR.jl.git")


    

    




INFO: Cloning SSBR from https://github.com/reworkhow/SSBR.jl.git
INFO: Computing changes...

In [2]:

    

using SSBR

ped,A_Mats,numSSBayes = calc_Ai("example/ped.txt","example/genotype.ID")
df    = read_genotypes("example/genotype.txt",numSSBayes,centering=true);


    

In [4]:

    

M_Mats = make_MMats(df,A_Mats,ped)
y_Vecs = make_yVecs("example/phenotype.txt",ped,numSSBayes)
J_Vecs = make_JVecs(numSSBayes,A_Mats)
Z_Mats = make_ZMats(ped,y_Vecs,numSSBayes)
X_Mats, W_Mats = make_XWMats(J_Vecs,Z_Mats,M_Mats,numSSBayes);


    

In [ ]:

    

#Gibbs sampler
nIter  = 50000
vRes   = 1.0
vG     = 1.0
aHat,alphaHat,betaHat,epsiHat=ssGibbs(M_Mats,y_Vecs,J_Vecs,Z_Mats,X_Mats,W_Mats,A_Mats,numSSBayes,vRes,vG,nIter);


    

In [ ]:

    

#Mixed Model Equation
vRes   = 1.0
vG     = 1.0
aHat2,alphaHat2,betaHat2,epsiHat2=ssMME(M_Mats,y_Vecs,J_Vecs,Z_Mats,X_Mats,W_Mats,A_Mats,numSSBayes,vRes,vG);


    

In [ ]:

    

#check accuracy
df = readtable("example/bv.txt", eltypes =[UTF8String, Float64], separator = ' ',header=false)
a  = Array(Float64,numSSBayes.num_ped)
for (i,ID) in enumerate(df[:,1])
     j = ped.idMap[ID].seqID
     a[j] = df[i,2]
end
cor(a,aHat)