debug_0702

##### do dosage vcf

plink2 --bfile eur_hla_prot --recode vcf --out eur_hla_prot
read.delim("eur_hla_prot.vcf",skip=6)->x
x[,10:ncol(x)]->x2
sapply(strsplit(colnames(x2),"_"),"[[",2)->id
read.table("/well/todd/users/xnc303/ukbb/olink/pheno_lodna",header=T)->pheno
x2[,match(pheno[,2],id)]->x3
x3->x4
for(i in 1:nrow(x3)){
gsub("0/0",0,x3[i,])->tmp
gsub("0/1",1,tmp)->tmp2
gsub("1/1",2,tmp2)->x4[i,]
print(i)}
rownames(x4)<-x$ID
colnames(x4)<-id
x4->dosage
save(dosage,file="dosage_eur.Rd")

#### troubleshoot HLA C 0702

load("/well/todd/users/xnc303/ukbb/imputed/dosage_eur.Rd")
read.table("/well/todd/users/xnc303/ukbb/olink/pheno_lodna",header=T)->pheno
read.table("/well/todd/users/xnc303/ukbb/olink/cov3_pc10",header=F)->cov

pheno[,"kir2dl3"]->kir
as.numeric(unlist(dosage["HLA_C*07:02",]))->test0702
as.numeric(unlist(dosage["HLA_C*07",]))->test07
cov[,4:ncol(cov)]->cov3
lm(kir~test0702+test07+V4+V5+V6+V7+V8+V9+V10+V11+V12+V13+V14+V15+V16+V17+V18+V19,data=cov3)->test