## CD-1 PFOA/GenX gestational exposure and latent health outcomes study ## PND22 necropsy data ## Body weight, liver weight, relative liver weight ## 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/PND22BWLWQC.csv") x$ID <-as.factor(x$ID) x$Dam.ID<-as.factor(x$Dam.ID) x$Group<-as.factor(x$Group) str(x) p22necrop<-x names(p22necrop) p22necrop.summary.stats<-p22necrop%>% group_by(Group,Sex)%>% summarise( bw.mean=mean(BW, na.rm=T), bw.sd=sd(BW, na.rm=T), liv.mean=mean(LW, na.rm=T), liv.sd=sd(LW, na.rm=T), rel.liv.mean=mean(RelLivWt, na.rm=T), rel.liv.sd=sd(RelLivWt, na.rm=T)) p22necrop.summary.stats write.csv(p22necrop.summary.stats, "PND22Necropsy Weights Summary Statistics.csv",row.names = F) ### Statistical Analyses ## Statistical analysis ## Males p22m<-subset(p22necrop, Sex=="M") p22f<-subset(p22necrop, Sex=="F") ## Female BW summary(glht(aov(BW~Group,data=p22f), linfct=mcp(Group="Dunnett"))) ## No differences ## Female LW summary(glht(aov(LW~Group,data=p22f), linfct=mcp(Group="Dunnett"))) ## No differences ## Female RelLivWt summary(glht(aov(RelLivWt~Group,data=p22f), linfct=mcp(Group="Dunnett"))) ## No differences (Vehicle vs 1.0 mg/kg PFOA p=0.0964) ## Male, BW summary(glht(aov(BW~Group,data=p22m), linfct=mcp(Group="Dunnett"))) ## No differences ## Male LW summary(glht(aov(LW~Group,data=p22m), linfct=mcp(Group="Dunnett"))) ## No differences ## Male RelLivWt summary(glht(aov(RelLivWt~Group,data=p22m), linfct=mcp(Group="Dunnett"))) ## Sig diff control vs PFOA 1.0 mg/kg (p=0.0168)