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AdvGeneMap2017Commands

14 bytes added, 20:44, 4 January 2017
__NOTITLE__
 
==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
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
==GWAS Data QC==
 
plink --file GWAS --noweb
plink --file GWAS --mind 0.10 --recode --out GWAS_clean_mind --noweb
q()
plink --file GWAS_clean3 --exclude HWE_out.txt --recode --out GWAS_clean4 --noweb
 
==GWAS Control Substructure==
 
plink --file GWAS_clean4 --genome --mds-plot 10 --noweb
R