## CD-1 PFOA/GenX gestational exposure and latent health outcomes study ## Week 12 Bruker ## Fat:lean and percent fat ## 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/Week12BrukerEDIT.csv") x$ID <-as.factor(x$ID) x$Group<-as.factor(x$Group) str(x) w12bruker<-x names(w12bruker) w12bruker.summary.stats<-w12bruker%>% group_by(Group,Sex,Diet)%>% summarise( BW.mean=mean(BW, na.rm=T), BW.sd=sd(BW, na.rm=T), fat.mean=mean(fat, na.rm=T), fat.sd=sd(fat, na.rm=T), fluid.mean=mean(fluid, na.rm=T), fluid.sd=sd(fluid, na.rm=T), lean.mean=mean(lean, na.rm=T), lean.sd=sd(lean, na.rm=T), fatlean.mean=mean(fatlean, na.rm=T), fatlean.sd=sd(fatlean, na.rm=T), percentfat.mean=mean(percentfat, na.rm=T), percentfat.sd=sd(percentfat, na.rm=T), percentfluid.mean=mean(percentfluid, na.rm=T), percentfluid.sd=sd(percentfluid, na.rm=T), percentlean.mean=mean(percentlean, na.rm=T), percentlean.sd=sd(percentlean, na.rm=T)) w12bruker.summary.stats write.csv(w12bruker.summary.stats, "Week12 Bruker Summary Statistics.csv",row.names = F) ### Statistical Analyses ## Statistical analysis ## Males w12m<-subset(w12bruker, Sex=="M") w12f<-subset(w12bruker, Sex=="F") w12mhf<-subset(w12m, Diet=="H") w12mlf<-subset(w12m, Diet=="L") w12fhf<-subset(w12f, Diet=="H") w12flf<-subset(w12f, Diet=="L") w12fveh<-subset(w12f, Group=="Control") w12mveh<-subset(w12m, Group=="Control") ## Male High Fat Body Weight summary(glht(aov(BW~Group,data=w12mhf), linfct=mcp(Group="Dunnet"))) ## No differences ## Male High Fat fat summary(glht(aov(fat~Group,data=w12mhf), linfct=mcp(Group="Dunnett"))) ## No differences ## Male High Fat fluid summary(glht(aov(fluid~Group,data=w12mhf), linfct=mcp(Group="Dunnett"))) ## no differences ## Male High Fat lean summary(glht(aov(lean~Group,data=w12mhf), linfct=mcp(Group="Dunnett"))) ## no differences ## Male High Fat fat:lean summary(glht(aov(fatlean~Group,data=w12mhf), linfct=mcp(Group="Dunnett"))) ## No differences ## Male High Fat percent fat summary(glht(aov(percentfat~Group,data=w12mhf), linfct=mcp(Group="Dunnett"))) ##no differences ## Male High Fat percent fluid summary(glht(aov(percentfluid~Group,data=w12mhf), linfct=mcp(Group="Dunnett"))) ## no differences ## Male High Fat percent lean summary(glht(aov(percentlean~Group,data=w12mhf), linfct=mcp(Group="Dunnett"))) ## No differences ## Male Low Fat Body Weight summary(glht(aov(BW~Group,data=w12mlf), linfct=mcp(Group="Dunnett"))) ## no differences ## Male Low Fat fat summary(glht(aov(fat~Group,data=w12mlf), linfct=mcp(Group="Dunnett"))) ## no differences ## Male Low Fat fluid summary(glht(aov(fluid~Group,data=w12mlf), linfct=mcp(Group="Dunnett"))) ## no differeces ## Male Low Fat lean summary(glht(aov(lean~Group,data=w12mlf), linfct=mcp(Group="Dunnett"))) ## No differences ## Male Low Fat fat:lean summary(glht(aov(fatlean~Group,data=w12mlf), linfct=mcp(Group="Dunnett"))) ## no differences ## Male Low Fat percent fat summary(glht(aov(percentfat~Group,data=w12mlf), linfct=mcp(Group="Dunnett"))) ## no differences ## Male Low Fat percent fluid summary(glht(aov(percentfluid~Group,data=w12mlf), linfct=mcp(Group="Dunnett"))) ##no differences ## Male Low Fat percent lean summary(glht(aov(percentlean~Group,data=w12mlf), linfct=mcp(Group="Dunnett"))) ## no differences ## Female High Fat Body Weight summary(glht(aov(BW~Group,data=w12fhf), linfct=mcp(Group="Dunnett"))) ## No differences ## Female High Fat fat summary(glht(aov(fat~Group,data=w12fhf), linfct=mcp(Group="Dunnett"))) ## No differences ## Female High Fat fluid summary(glht(aov(fluid~Group,data=w12fhf), linfct=mcp(Group="Dunnett"))) ## no differences ## Female High Fat lean summary(glht(aov(lean~Group,data=w12fhf), linfct=mcp(Group="Dunnett"))) ##no differences ## Female High Fat fat:lean summary(glht(aov(fatlean~Group,data=w12fhf), linfct=mcp(Group="Dunnett"))) ## No differences ## Female High Fat percent fat summary(glht(aov(percentfat~Group,data=w12fhf), linfct=mcp(Group="Dunnett"))) ##no differences ## Female High Fat percent fluid summary(glht(aov(percentfluid~Group,data=w12fhf), linfct=mcp(Group="Dunnett"))) ##no differences ## Female High Fat percent lean summary(glht(aov(percentlean~Group,data=w12fhf), linfct=mcp(Group="Dunnett"))) ## No differences ## Female Low Fat Body Weight summary(glht(aov(BW~Group,data=w12flf), linfct=mcp(Group="Dunnett"))) ## No differences ## Female Low Fat fat summary(glht(aov(fat~Group,data=w12flf), linfct=mcp(Group="Dunnett"))) ## No differences ## Female Low Fat fluid summary(glht(aov(fluid~Group,data=w12flf), linfct=mcp(Group="Dunnett"))) ##no differences ## Female Low Fat lean summary(glht(aov(lean~Group,data=w12flf), linfct=mcp(Group="Dunnett"))) ##no differences ## Female Low Fat fat:lean summary(glht(aov(fatlean~Group,data=w12flf), linfct=mcp(Group="Dunnett"))) ## No differences ## Female Low Fat percent fat summary(glht(aov(percentfat~Group,data=w12flf), linfct=mcp(Group="Dunnett"))) ##no differences ## Female Low Fat percent fluid summary(glht(aov(percentfluid~Group,data=w12flf), linfct=mcp(Group="Dunnett"))) ##no differences ## Female Low Fat percent lean summary(glht(aov(percentlean~Group,data=w12flf), linfct=mcp(Group="Dunnett"))) ## No differences summary(glht(aov(fat~Diet, data=w12fveh))) ##p=0.00563 summary(glht(aov(fat~Diet, data=w12mveh))) ##p<0.0001 summary(glht(aov(fluid~Diet, data=w12fveh))) ##p=0.00454 summary(glht(aov(fluid~Diet, data=w12mveh))) ##p<0.0001