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
interest = dosage[which(dosage$SNP=='rs715586'),]
interest
==PLINK_R==
Introduction
snp.data = dbp[,c("affection", "rs1112")]
summary(snp.data)
snp.data[,"rs1112"]<-as.numeric(snp.data[,"rs1112"])-1<br /> summary(snp.data)<br /> result.all=glm(affection ~ rs1112, family=binomial("logit"), data=snp.data)<br /> dev.all = anova(result.all, test="Chi")<br /> summary(result.all) print(dev.all)<br /> snp.data = dbp[,c("affection","trait","sex","age","rs1112","rs1117")]<br /> summary(snp.data)<br /> snp.data[,"rs1112"]<-as.numeric(snp.data[,"rs1112"])-1<br /> snp.data[,"rs1117"]<-as.numeric(snp.data[,"rs1117"])-1<br /> result.adj = glm(affection ~ sex + rs1112, family=binomial("logit"), data=snp.data)<br /> summary(result.adj)
result.adj = glm (affection ~ age + rs1112 , family=binomial("logit"), data=snp.data)
summary(result.adj)
gws_unadj = aff_unadj[which(aff_unadj$P < 0.0000001),]
gws_unadj
gws_adjusted = aff_C1C2[which(aff_C1C2$P < 0.0000001),] gws_adjusted
q()
pseq myproj assoc --tests skat --phenotype BMI --covar SEX --mask include="DP>14" geno=DP:ge:11 file=YRI hwe=5.7e-7:1 "mac=1 maf=0.01" loc.group=refseq > SKAT_YRI.result
head -20 SKAT_YRI.result
cat SKAT_YRI.result | grep SKAT | grep -v "P=NA" | sort -k6 | head -15 ==RV-TDT exercise==
vtools init rvtdt
vtools import --format vcf data/data.vcf --build hg19
do
echo "runing rvTDT on gene "${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
# clean
rm -r exercise_proj* genes/* bgl* linkage* recode12* pre_beagle* vat_export.*
==SEQPower==
spower -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 mypeds.ped –window 2 –reference 1 2 1 1
unphased all.ped -window 2 -LD
unphased all.ped -window 2 -LD >> results.txt==VAT==
vtools -h
vtools init VATDemo