library(tidyverse)
met <- read_csv('https://denvirlab.marshall.edu/BMR617-2023/data/TH-B6-metabolic.csv') %>%
  separate(MouseID, sep="-", into=c("Strain", "Diet", "ID")) %>%
  mutate(Strain = as.factor(Strain), Diet = as.factor(Diet))

met.chow <- met %>% filter(Diet == "Chow")

t.test(Cholesterol ~ Strain, data = met.chow, var.equal = TRUE)

met.chow <- met.chow %>% mutate(CodedStrain = ifelse(Strain=="B6", 0, 1))
summary(lm(Cholesterol ~ CodedStrain, data = met.chow))

ggplot(met.chow, aes(x=CodedStrain, y=Cholesterol)) + geom_point()

summary(lm(Cholesterol ~ Strain, data = met.chow))

contrasts(met.chow$Strain)

rwd <- read_csv("https://denvirlab.marshall.edu/BMR617-2023/data/RenalWesternData.csv")
sgk1 <- filter(rwd, Protein=="SGK1")
sgk1.pt.tt <- lm(Expression ~ TissueType + Patient, data=sgk1)
summary(sgk1.pt.tt)
t.test(Expression ~ TissueType, paired=T, data=rwd %>% filter(Protein=="SGK1"))


met.b6 <- filter(met, Strain=="B6")

contrasts(met.b6$Diet)
fit.diet <- lm(Cholesterol ~ Diet, data=met.b6)
fit.diet
summary(fit.diet)

aov.diet <- aov(Cholesterol ~ Diet, data=met.b6)
aov.diet
summary(aov.diet)