==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$SNP=='rs715586'),]
interest
==PLINK_R==
Introduction
head -20 SKAT_YRI.result
cat SKAT_YRI.result | grep SKAT | grep -v "P=NA" | sort -k6 | head -15==RV-TDT exercise==
vtools init rvtdt
vtools import --format vcf data/data.vcf --build hg19
do
echo "runing rvTDT on gene "${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
rm -r exercise_proj* genes/* bgl* linkage* recode12* pre_beagle* vat_export.*
==SEQPower==
spower -h
spower LOGIT -h
for i in 1 1.5 2 2.5 3 3.5 4; do
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
==VAT==
vtools -h
vtools init VATDemo