HeritabilityTest/Create.kinship.1.R at master · jrahimik/HeritabilityTest · GitHub

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data.uni = read.table("data.uni.1.txt",header=TRUE)
data.biv = read.table("data.biv.1.txt",header=TRUE)

kin1 = NULL
kin2 = NULL

compteur=1

for (fam in unique(data.uni$fam.id))
{
len = sum(data.uni$fam.id==fam)
ind = data.uni$ind.id[data.uni$fam.id==fam]

V1 = diag(rep(0.5,len))
V2 = diag(rep(0.5,len))

for(i in 1:(len-1))
{
for(j in (i+1):len)
{
cond1 = (data.biv$fam.id==fam)&(data.biv$ind.id1==ind[i])&(data.biv$ind.id2==ind[j])
cond2 = (data.biv$fam.id==fam)&(data.biv$ind.id2==ind[i])&(data.biv$ind.id1==ind[j])
cond = cond1 | cond2
indice = which(cond)
V1[i,j] = (data.biv$kinship.ff)[indice]
V1[j,i] = V1[i,j]
V2[i,j] = (data.biv$kinship.fm)[indice]+(data.biv$kinship.mf)[indice]+(data.biv$kinship.mm)[indice]
V2[j,i] = V2[i,j]
}
}
kin1[[compteur]]=V1
kin2[[compteur]]=V2
compteur=compteur+1
}