cd GWAS_part2
plink --file GWAS --noweb
plink –--file GWAS –--mind 0.10 –--recode –--out GWAS_clean_mind --noweb plink –--file GWAS_clean_mind –--maf 0.05 –--recode –--out MAF_greater_5 --noweb plink –--file GWAS_clean_mind –--exclude MAF_greater_5.map –--recode –--out MAF_less_5 --noweb
plink --file MAF_greater_5 --geno 0.05 --recode --out MAF_greater_5_clean --noweb
plink --file MAF_less_5 --geno 0.01 --recode --out MAF_less_5_clean --noweb
plink --file GWAS_MAF_clean --mind 0.03 --recode --out GWAS_clean2 --noweb
R
plink –--file GWAS_clean2 –--check-sex –--out GWAS_sex_checking --noweb
sexcheck = read.table("GWAS_sex_checking.sexcheck", header=T)
names(sexcheck)
sex_problem
q()
plink –--file GWAS_clean2 –--genome –--out duplicates --noweb
R
dups = read.table(“duplicates.genome”, header = T)
q()
plink --file GWAS_clean2 --remove IBS_excluded.txt --recode --out GWAS_clean3 --noweb
plink –--file GWAS_clean3 –--het --noweb
R
Dataset <- read.table("plink.het", header=TRUE, sep="", na.strings="NA", dec=".",
dev.off()
q()
plink –--file GWAS_clean3 –--pheno pheno.txt –--pheno-name Aff –--hardy --noweb
R
hardy = read.table(“plink.hwe”, header = T)
hwe_prob
q()
plink –--file GWAS_clean3 –--exclude HWE_out.txt –--recode –--out GWAS_clean4 --noweb
Multifactorial
GWAS Control Substructure
plink –--file GWAS_clean4 –--genome –--mds-plot 10
R
mydata = read.table("mds_components.txt", header=T)
dev.off()
q()
plink –--file GWAS_clean4 –--pheno pheno.txt –--pheno-name Aff –--logistic --adjust –--out unadj --noweb plink –--file GWAS_clean4 –--pheno pheno.txt –--pheno-name Aff –--covar plink.mds –--covar-name C1 –--logistic –--adjust –--out C1 --noweb plink –--file GWAS_clean4 –--pheno pheno.txt –--pheno-name Aff –--covar plink.mds –--covar-name C1-C2 –--logistic –--adjust –--out C1-C2 --noweb
R
broadqq <-function(pvals, title)