plink --file chr22_imputation_ex

plink --file chr22_imputation_ex --maf 0.01 --mind 0.02 --geno 0.05 --hwe 0.001 --out qc_check

plink --file chr22_imputation_ex --maf 0.01 --min 0.02 --geno 0.05 --hwe 0.001 --recode --out chr22_clean1

plink --file chr22_clean1 --maf 0.01 --mind 0.02 --geno 0.05 --hwe 0.001 --out qc_check_2

plink --file chr22_clean1 --filter-cases --hwe 0.001 --recode --out chr22_cases_clean

plink --file chr22_clean1 --filter-controls --recode --out chr22_controls_clean

plink --file chr22_controls_clean --merge chr22_cases_clean.ped chr22_cases_clean.map --hwe 0.001 --recode --out chr22_all_clean

plink --file chr22_all_clean --logistic --out chr22_all_clean_geno

# start up R
R

# now in R
"mydata = read.table(""chr22_all_clean_geno.assoc.logistic"", header=T)"

names(mydata)

"plot(mydata$BP, -log10(mydata$P))"

"smallp = mydata[which(mydata$P < 1E-6),]"
smallp

"smallp = smallp[order(smallp$BP),]"
smallp
q()

#not in R anymore

plink -dosage chr22_HIHII_dose_mach4plink.txt.gz Zin -fam chr22_imputation_ex.fam -map chr22_imputed_snps_positions.map --out chr22_HIHII_dosage

R

# now in R
"dosage = read.table(""chr22_HIHII_dosage.assoc.dosage"", header= T)"
names(dosage)

"plot(dosage$BP, -log10(dosage$P))"

"dosagep = dosage[which(dosage$P < 1E-6),]"
"dosagep = dosagep[order(dosagep$BP),]"
dosagep

"interest = dosage[which(dosage$SNP=='rs7372328'),]"
interest
