results(testb.qt)$P1df[results(testb.qt)$P1df < alpha]
results(testb.qt)$Pc1df[results(testb.qt)$Pc1df < alpha]
===GxG Interaction===
./plink --noweb --ped simcasecon.ped --map simcasecon.map --assoc
./plink --noweb --ped simcasecon.ped --map simcasecon.map --fast-epistasis
./plink --noweb --ped simcasecon.ped --map simcasecon.map --fast-epistasis --caseonly
./plink --noweb --ped simcasecon.ped --map simcasecon.map --epistasis
./plink --noweb --ped simcasecon.ped --map simcasecon.map --recodeA --out recoded
./plink --noweb --ped simcasecon.ped --map simcasecon.map --make-bed --out cassiformat
R
# The following commands are in the R environment
je <-read.table("cassi.out", header=T)
je
library(ORMDR)
recoded<-read.table("recoded.raw", header=T)
head(recoded)
newdata<-recoded[7:106]
ormdrdata<-cbind(newdata,recoded$PHENOTYPE-1)
names(ormdrdata)[101]<-"casestatus"
head(ormdrdata)
mdr1<-mdr.c(ormdrdata, colresp=101, cs=1, combi=1, cv.fold = 10)
mdr1$min.comb
mdr2<-mdr.c(ormdrdata, colresp=101, cs=1, combi=2, cv.fold = 10)
mdr2$min.comb
mdr3<-mdr.c(ormdrdata, colresp=101, cs=1, combi=3, cv.fold = 10)
mdr3$min.comb
mdr1$test.erate
mdr2$test.erate
mdr3$test.erate
mdr1mean<-mean(mdr1$test.erate)
mdr2mean<-mean(mdr2$test.erate)
mdr3mean<-mean(mdr3$test.erate)
mdr1mean
mdr2mean
mdr3mean
mdr2$best.combi
mdr2$min.comb
mdr3$best.combi
mdr3$min.comb
logreg12<-glm(casestatus ~ factor(snp1_2)*factor(snp2_1), family=binomial,
data=ormdrdata)
summary(logreg12)
anova(logreg12)
pchisq(701.68,4,lower.tail=F)
pchisq(703.82,8,lower.tail=F)
logreg345<-glm(casestatus ~ factor(snp3_2)*factor(snp4_2)*factor(snp5_2),
family=binomial, data=ormdrdata)
summary(logreg345)
anova(logreg345)
pchisq(45.6,8,lower.tail=F)
q()
### The following commands are in the linux shell
./BEAM3 beam3data.txt -o beam3results
./BEAM3 beam3data.txt -o beam3results -T 10
===Plink - Part 1 - Data QC===