Changes
From Statistical Genetics Courses
==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==
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()
Multiple Testing
rm -r exercise_proj* genes/* bgl* linkage* recode12* pre_beagle* vat_export.*
==SEQPower==
spower -h
spower LOGIT -h
