## CD-1 PFOA/GenX gestational exposure and latent health outcomes study
## PND22 lipid panel
## 
## HAC 01/22/2020 (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/QCPND22LipidPanel.csv")
x$ID <-as.factor(x$ID)
x$Group<-as.factor(x$Group)

str(x)

p22lipid<-x


names(p22lipid)

p22lipid.summary.stats<-p22lipid%>%
  group_by(Group,Sex)%>%
  summarise(
    Trig.mean=mean(Trig, na.rm=T),
    Trig.sd=sd(Trig, na.rm=T),
    HDL.mean=mean(HDL, na.rm=T),
    HDL.sd=sd(HDL, na.rm=T),
    Chol.mean=mean(Chol, na.rm=T),
    Chol.sd=sd(Chol, na.rm=T),
    LDL.mean=mean(LDL, na.rm=T),
    LDL.sd=sd(LDL, na.rm=T),
    HDLLDL.mean=mean(HDLLDL, na.rm=T),
    HDLLDL.sd=sd(HDLLDL, na.rm=T))
p22lipid.summary.stats


write.csv(p22lipid.summary.stats, "PND22 Lipid Panel Summary Statistics.csv",row.names = F)


### Statistical Analyses

## Statistical analysis
## Males

p22m<-subset(p22lipid, Sex=="M")
p22f<-subset(p22lipid, Sex=="F")

## Female Trig
summary(glht(aov(Trig~Group,data=p22f), linfct=mcp(Group="Dunnett")))
## Sig diff for all groups: p <0.0001 for GenX 0.2, 1.0, 2.0 and PFOA 1.0, p=0.000717 for PFOA 0.1

## Female HDL
summary(glht(aov(HDL~Group,data=p22f), linfct=mcp(Group="Dunnett")))
## No differences

## Female total cholesterol
summary(glht(aov(Chol~Group,data=p22f), linfct=mcp(Group="Dunnett")))
## No differences

## Female LDL
summary(glht(aov(LDL~Group,data=p22f), linfct=mcp(Group="Dunnett")))
## No differences

## Female HDL to LDL ratio
summary(glht(aov(HDLLDL~Group,data=p22f), linfct=mcp(Group="Dunnett")))
## Sig dif between control and GenX 2.0 (p=0.00816)

## Male Trig
summary(glht(aov(Trig~Group,data=p22m), linfct=mcp(Group="Dunnett")))
## Sig diff for 1.0 mg/kg GenX (p=0.02341) 2.0 GenX (p=0.00588) and 1.0 PFOA (p=0.00517)

## Male HDL
summary(glht(aov(HDL~Group,data=p22m), linfct=mcp(Group="Dunnett")))
## No differences

## Male total cholesterol
summary(glht(aov(Chol~Group,data=p22m), linfct=mcp(Group="Dunnett")))
## No differences, trend for GenX 1.0 mg/kg PFOA vs control (p=0.0711)

## Male LDL
summary(glht(aov(LDL~Group,data=p22m), linfct=mcp(Group="Dunnett")))
## Difference in 1.0 mg/kg PFOA vs control (p=0.0473), trend in GenX 1.0 mg/kg vs control (p=0.0848)

## Male HDL to LDL ratio
summary(glht(aov(HDLLDL~Group,data=p22m), linfct=mcp(Group="Dunnett")))
## No differences