## CD-1 PFOA/GenX gestational exposure and latent health outcomes study
## Week 18 Glucose and Insulin
## Glucose (mg/dL) Insulin (pg/mL) and QUICKI
## HAC 01/26/2020 (w/ QC data)

## Load packages (needs to be done every time R is opened)
library(dplyr)
library(lme4)
library(ggplot2)
library(multcomp)
library(tidyverse)
library(clinfun)

# Set your working directory (replace this example with your file folder destination)
setwd("/Users/harliecope/Desktop/GenX:PFOA Study/GenX PFOA Mouse Study/GenXPFOA Study")

# Read in your files
x<- read_csv("~/Desktop/GenX:PFOA Study/GenX PFOA Mouse Study/QC Data Files/csv for R/QCGluIns.csv")
x$ID <-as.factor(x$ID)
x$Group<-as.factor(x$Group)


str(x)

w18glu<-x


names(w18glu)

w18glu.summary.stats<-w18glu%>%
  group_by(Group,Sex,Diet)%>%
  summarise(
    Glu.mean=mean(Glu, na.rm=T),
    Glu.sd=sd(Glu, na.rm=T),
    Insulin.mean=mean(Insulin, na.rm=T),
    Insulin.sd=sd(Insulin, na.rm=T),
    QUICKI.mean=mean(QUICKI, na.rm=T),
    QUICKI.sd=sd(QUICKI, na.rm=T))
w18glu.summary.stats


write.csv(w18glu.summary.stats, "Week18 Glucose and Insulin Summary Statistics.csv",row.names = F)


### Statistical Analyses

## Statistical analysis
## Males

w18m<-subset(w18glu, Sex=="M")
w18f<-subset(w18glu, Sex=="F")

w18mhf<-subset(w18m, Diet=="H")
w18mlf<-subset(w18m, Diet=="L")
w18fhf<-subset(w18f, Diet=="H")
w18flf<-subset(w18f, Diet=="L")

## Male High Fat Glucose 
summary(glht(aov(Glu~Group,data=w18mhf), linfct=mcp(Group="Dunnett")))
## No differences

## Male High Fat Insulin
summary(glht(aov(Insulin~Group,data=w18mhf), linfct=mcp(Group="Dunnett")))
## Difference in 1.0 mg/kg GenX compared to control (p=0.00364)

## Male High Fat QUICKI
summary(glht(aov(QUICKI~Group,data=w18mhf), linfct=mcp(Group="Dunnett")))
## No differences

## Male Low Fat Glucose
summary(glht(aov(Glu~Group,data=w18mlf), linfct=mcp(Group="Dunnett")))
## No differences

## Male Low Fat Insulin
summary(glht(aov(Insulin~Group,data=w18mlf), linfct=mcp(Group="Dunnett")))
## Difference in control vs 2.0 mg/kg GenX (p=0.0211)

## Male Low Fat QUICKI
summary(glht(aov(QUICKI~Group,data=w18mlf), linfct=mcp(Group="Dunnett")))
## Difference between control and GenX 2.0 mg/kg (p=0.0140) and PFOA 1.0 mg/kg (p=0.0176) (1.0 mg/kg GenX p=0.085)


## Female High Fat Glucose
summary(glht(aov(Glu~Group,data=w18fhf), linfct=mcp(Group="Dunnett")))
## No differences Genx 0.2 vs control p=0.0525

## Female High Fat Insulin
summary(glht(aov(Insulin~Group,data=w18fhf), linfct=mcp(Group="Dunnett")))
## Difference between control and PFOA 1.0 mg/kg (p=0.0112)

## Female High Fat QUICKI
summary(glht(aov(QUICKI~Group,data=w18fhf), linfct=mcp(Group="Dunnett")))
## No differences, control vs 0.1 mg/kg PFOA p=0.0793

## Female Low Fat Glucose
summary(glht(aov(Glu~Group,data=w18flf), linfct=mcp(Group="Dunnett")))
## No Differences

## Female Low Fat Insulin
summary(glht(aov(Insulin~Group,data=w18flf), linfct=mcp(Group="Dunnett")))
## No differences

## Female Low Fat QUICKI
summary(glht(aov(QUICKI~Group,data=w18flf), linfct=mcp(Group="Dunnett")))
## No differences