Changes
From Statistical Genetics Courses
/* GxG Interaction */
===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 --caseonlycase-only
./plink --noweb --ped simcasecon.ped --map simcasecon.map --epistasis
./plink --noweb --ped simcasecon.ped --map simcasecon.map --recodeA --out recoded
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$test.erate
mdr3$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===
