Changes
From Statistical Genetics Courses
/* Regression exercise */
In R:
load("dbp.R")<br data-attributes="%20/" /> ls()<br data-attributes="%20/" />dbp[1:5,]<br data-attributes="%20/" />#<br data-attributes="%20/" />result.snp12 = glm (affection ~ rs1112, family=binomial("logit"), data=dbp)<br data-attributes="%20/" />print (result.snp12)<br data-attributes="%20/" />print ( class (result.snp12) )<br data-attributes="%20/" />print ( summary(result.snp12) )<br data-attributes="%20/" />#<br data-attributes="%20/" />dev.geno = anova (result.snp12, test="Chi")<br data-attributes="%20/" />lrt.pvalue = pchisq(dev.geno[dim(dev.geno)[1],"Deviance"],<br data-attributes="%20/" /> df=2, ncp=0, FALSE)<br data-attributes="%20/" />print ( lrt.pvalue )<br data-attributes="%20/" />#<br data-attributes="%20/" />print ( summary(result.snp12)$coefficients )<br data-attributes="%20/" />snp.beta = summary(result.snp12)$coefficients[2:3,1]<br data-attributes="%20/" />print ( snp.beta )<br data-attributes="%20/" />print ( exp(snp.beta) )<br data-attributes="%20/" />ci = confint (result.snp12)<br data-attributes="%20/" />print (ci)<br data-attributes="%20/" />print ( exp(ci) )<br data-attributes="%20/" />#<br data-attributes="%20/" />snp.data = dbp[,c("affection", "rs1112")]<br data-attributes="%20/" />summary(snp.data)<br data-attributes="%20/" />snp.data[,"rs1112"]<- as.numeric(snp.data[,"rs1112"]) - 1<br />summary(snp.data)<br data-attributes="%20/" />#<br data-attributes="%20/" />result.all = glm (affection ~ rs1112, family=binomial("logit"),<br data-attributes="%20/" /> data=snp.data)<br data-attributes="%20/" />dev.all = anova (result.all, test="Chi")<br data-attributes="%20/" />summary(result.all)<br data-attributes="%20/" />print(dev.all)<br data-attributes="%20/" />#<br data-attributes="%20/" />snp.data = dbp[,c("affection", "trait","sex", "age", "rs1112", "rs1117")]<br data-attributes="%20/" />summary(snp.data)<br data-attributes="%20/" />snp.data[,"rs1112"]<- as.numeric(snp.data[,"rs1112"]) - 1<br />snp.data[,"rs1117"] <- as.numeric(snp.data[,"rs1117"]) - 1
#<br data-attributes="%20/" />result.adj = glm (affection ~ sex + rs1112 , family=binomial("logit"),<br data-attributes="%20/" /> data=snp.data)<br data-attributes="%20/" />summary(result.adj)<br data-attributes="%20/" />#<br data-attributes="%20/" />result.adj = glm (affection ~ age + rs1112 , family=binomial("logit"),<br data-attributes="%20/" /> data=snp.data)<br data-attributes="%20/" />summary(result.adj)<br data-attributes="%20/" />#<br data-attributes="%20/" />result.adj = glm (affection ~ sex + age + rs1112, family=binomial("logit"),<br data-attributes="%20/" /> data=snp.data)<br data-attributes="%20/" />summary(result.adj)<br data-attributes="%20/" />#<br data-attributes="%20/" />result.adj = glm (affection ~ rs1117 + rs1112, family=binomial("logit"),<br data-attributes="%20/" /> data=snp.data)<br data-attributes="%20/" />summary(result.adj)<br data-attributes="%20/" />anova (result.adj, test="Chi")<br data-attributes="%20/" />result.adj = glm (affection ~ rs1112 + rs1117, family=binomial("logit"),<br data-attributes="%20/" /> data=snp.data)<br data-attributes="%20/" />summary(result.adj)<br data-attributes="%20/" />anova (result.adj, test="Chi")<br data-attributes="%20/" />#<br data-attributes="%20/" />result.adj = lm (trait ~ rs1112, data=snp.data)<br data-attributes="%20/" />summary(result.adj)<br data-attributes="%20/" />result.adj = lm (trait ~ sex + rs1112, data=snp.data)<br data-attributes="%20/" />summary(result.adj)<br data-attributes="%20/" />#<br data-attributes="%20/" />result.inter = glm (affection ~ sex * rs1112, family=binomial("logit"),<br data-attributes="%20/" /> data=snp.data)<br data-attributes="%20/" />summary(result.inter)<br data-attributes="%20/" />result.inter = glm (affection ~ age * rs1112, family=binomial("logit"),<br data-attributes="%20/" /> data=snp.data)<br data-attributes="%20/" />summary(result.inter)<br data-attributes="%20/" />#<br data-attributes="%20/" />result.inter = glm (affection ~ rs1112 * rs1117, family=binomial("logit"),<br data-attributes="%20/" /> data=snp.data)<br data-attributes="%20/" />summary(result.inter)<br data-attributes="%20/" />#<br data-attributes="%20/" />q()
