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==
plink --file chr22_imputation_ex --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$P < 0.0000001),] gws_adjusted
q()
do
echo "runing rvTDT on gene "${g}
rvTDT exercise_proj -G ./genes/${g}.tped -P ./data/rvtdt.phen -M ./genes/${g}.map --adapt 500 --alpha 0.00001 --permut 2000 --lower_cutoff 0 --upper_cutoff 100 -- minVariants 3 --maxMissRatio 1
done
# Answer
spower LOGIT Kryukov2009European1800.sfs --sample_size 1000 --OR_rare_detrimental $i --method "CFisher --name CMC$i" --title FixedOR$i -r 100 -j 4 -l 1 -o exercise2
done<br />spower show exercise2.SEQPowerDB LOGIT method power title==Unphased==
unphased.sh
unphased mypeds.ped –marker 1 2 3 –missing –permutation 10
unphased all.ped -window 2 -LD
unphased all.ped -window 2 -LD >> results.txt
vtools -h
vtools init VATDemo