## CD-1 PFOA/GenX gestational exposure and latent health outcomes study
## Week 14 GTT AUC and baseline glucose
## 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)

# 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/Week14GTTAUC_merged.csv")
x$ID <-as.factor(x$ID)
x$Group<-as.factor(x$Group)


str(x)

w14GTT<-x


names(w14GTT)

w14GTT.summary.stats<-w14GTT%>%
  group_by(Group,Sex,Diet)%>%
  summarise(
    auc.trap.mean=mean(auc.trap, na.rm=T),
    auc.trap.sd=sd(auc.trap, na.rm=T),
    X0.mean=mean(X0, na.rm=T),
    X0.sd=sd(X0, na.rm=T))
w14GTT.summary.stats


write.csv(w14GTT.summary.stats, "Week14 GTT Summary Statistics.csv",row.names = F)


### Statistical Analyses

## Statistical analysis
## Males

w14m<-subset(w14GTT, Sex=="M")
w14f<-subset(w14GTT, Sex=="F")

w14mhf<-subset(w14m, Diet=="H")
w14mlf<-subset(w14m, Diet=="L")
w14fhf<-subset(w14f, Diet=="H")
w14flf<-subset(w14f, Diet=="L")

w14fveh<-subset(w14f, Group=="Control")
w14mveh<-subset(w14m, Group=="Control")
## Male High Fat fasted glucose
summary(glht(aov(X0~Group,data=w14mhf), linfct=mcp(Group="Dunnett")))
## No differences

## Male High Fat AUC
summary(glht(aov(auc.trap~Group,data=w14mhf), linfct=mcp(Group="Dunnett")))
## No differences


## Male Low Fat fasted glucose
summary(glht(aov(X0~Group,data=w14mlf), linfct=mcp(Group="Dunnett")))
## No differences

## Male Low Fat auc
summary(glht(aov(auc.trap~Group,data=w14mlf), linfct=mcp(Group="Dunnett")))
## No differences

## Female High Fat fasted glucose
summary(glht(aov(X0~Group,data=w14fhf), linfct=mcp(Group="Dunnett")))
## No differences

## Female High Fat auc
summary(glht(aov(auc.trap~Group,data=w14fhf), linfct=mcp(Group="Dunnett")))
## No differences


## Female Low Fat fasted glucose
summary(glht(aov(X0~Group,data=w14flf), linfct=mcp(Group="Dunnett")))
## Difference in 1.0 mg/kg GenX vs control (p=0.0232)

## Female Low Fat auc
summary(glht(aov(auc.trap~Group,data=w14flf), linfct=mcp(Group="Dunnett")))
## No differences


summary(glht(aov(X0~Diet, data=w14fveh)))
##p=0.828
summary(glht(aov(X0~Diet, data=w14mveh)))
##p=0.0208
summary(glht(aov(auc.trap~Diet, data=w14fveh)))
##p=0.00195
summary(glht(aov(auc.trap~Diet, data=w14mveh)))
##p=0.000234