==GeneABEL==
plink --file GWAS_clean4 --pheno pheno.phen --pheno-name Aff --transpose --recode --out gwa_gabel --noweb
plink --file GWAS_clean4 --pheno pheno.phen --pheno-name systolic --transpose --recode --out gwa_gabel_qtl --noweb
plot(test.qt, col = "black")
add.plot(test.eg, col = "gray", pch = 3)
legend("topright", c("Original plot","After correction w/ EIGENSTRAT"), pch = c(1,3))==Imputation exercise==
==Imputation exercise==
plink --file chr22_imputation_ex --noweb
plink --file chr22_imputation_ex --maf 0.01 --mind 0.02 --geno 0.05 --hwe 0.001 --out qc_check --noweb
names(dosage)
plot(dosage$BP, -log10(dosage$P))
dosagep = dosage[which(dosage$P < 5E-8),] dosagep = dosagep[order(dosagep$BP),]
dosagep
interest = dosage[which(dosage$SNP=='rs715586'),]
interest
==PLINK_R==
Introduction
gws_unadj = aff_unadj[which(aff_unadj$P < 0.0000001),]
gws_unadj
gws_adjusted = aff_C1C2[which(aff_C1C2$P < 0.0000001),] gws_adjusted
q()
cat SKAT_YRI.result | grep SKAT | grep -v "P=NA" | sort -k6 | head -15
==SEQPowerRV-TDT exercise== for g in `ls rvtdt_exercise_data | grep tped | cut -d"." -f1` do echo "runing rvTDT on gene "${g} ./rvTDT exercise_proj -G ./rvtdt_exercise_data/${g}.tped \ -P ./rvtdt_exercise_data/rvtdt_exercise.phen \ -M ./rvtdt_exercise_data/${g}.map \ --adapt 500 --alpha 0.00001 --permut 2000 \ --lower_cutoff 0 --upper_cutoff 100 \ --minVariants 3 \ --maxMissRatio 1 done
==SEQPower==
spower -h
spower LOGIT -h
==Unphased==
unphased.sh
unphased mypeds.ped –marker 1 2 3 –missing –permutation 10
unphased mypeds.ped –window 2 –reference 1 2 1 1
unphased all.ped -window 2 -LD
unphased all.ped -window 2 -LD >> results.txt==VAT==
==VAT==
vtools -h
vtools init VATDemo