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prep_lmm.rawAFC.R
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library(data.table)
library(dplyr)
# read in data
genoF <- as.data.table(read.table("hap_blocks.freq", h=F, stringsAsFactors=F))
genoF$loc<- 1:nrow(genoF)
genoF_cov <- as.data.table(read.table("hap_blocks.cov", h=F, stringsAsFactors=F))
## calculate divergence from ancestor using Kelly and Hughes 2019 angular transformation
data=select(genoF, V1,V2)
genoF$Ancestral= rowMeans(data)
genoF<-genoF %>%
mutate(V3= V3 - Ancestral) %>%
mutate(V4= V4 - Ancestral) %>%
mutate(V5= V5 - Ancestral)%>%
mutate(V6= V6 - Ancestral)%>%
mutate(V7= V7 - Ancestral)%>%
mutate(V8= V8 - Ancestral)%>%
mutate(V9= V9 - Ancestral)%>%
mutate(V10= V10 - Ancestral)%>%
mutate(V11= V11 - Ancestral)%>%
mutate(V12= V12 - Ancestral)%>%
mutate(V13= V13 - Ancestral)%>%
mutate(V14= V14 - Ancestral)%>%
mutate(V15= V15 - Ancestral)%>%
mutate(V16= V16 - Ancestral)%>%
mutate(V17= V17 - Ancestral)%>%
mutate(V18= V18 - Ancestral)%>%
mutate(V19= V19 - Ancestral)%>%
mutate(V20= V20 - Ancestral)%>%
mutate(V21= V21 - Ancestral)%>%
mutate(V22= V22 - Ancestral)%>%
mutate(V23= V23 - Ancestral)%>%
mutate(V24= V24 - Ancestral)%>%
mutate(V25= V25 - Ancestral)%>%
mutate(V26= V26 - Ancestral)%>%
mutate(V27= V27 - Ancestral)%>%
mutate(V28= V28 - Ancestral)
## reformat
setDT(genoF)
genoF<-select(genoF,3:29)
MgenoF<-melt(genoF, id.vars ="loc")
MgenoF$variable<-as.character(MgenoF$variable)
MgenoF$Generation<-rep(NA,nrow(MgenoF))
MgenoF$Treat<-rep(NA,nrow(MgenoF))
MgenoF<- MgenoF %>%
mutate(variable = replace(variable, variable=="V3", "Control20")) %>%
mutate(variable = replace(variable, variable=="V4", "Control20")) %>%
mutate(variable = replace(variable, variable=="V5", "Control6")) %>%
mutate(variable = replace(variable, variable=="V6", "Control10")) %>%
mutate(variable = replace(variable, variable=="V7", "Control10")) %>%
mutate(variable = replace(variable, variable=="V8", "Control6")) %>%
mutate(variable = replace(variable, variable=="V9", "Control10")) %>%
mutate(variable = replace(variable, variable=="V10", "Control10")) %>%
mutate(variable = replace(variable, variable=="V11", "Treatment6")) %>%
mutate(variable = replace(variable, variable=="V12", "Treatment10")) %>%
mutate(variable = replace(variable, variable=="V13", "Treatment6")) %>%
mutate(variable = replace(variable, variable=="V14", "Treatment10")) %>%
mutate(variable = replace(variable, variable=="V15", "Treatment6")) %>%
mutate(variable = replace(variable, variable=="V16", "Treatment10")) %>%
mutate(variable = replace(variable, variable=="V17", "Treatment6")) %>%
mutate(variable = replace(variable, variable=="V18", "Treatment10")) %>%
mutate(variable = replace(variable, variable=="V19", "Treatment6")) %>%
mutate(variable = replace(variable, variable=="V20", "Treatment6")) %>%
mutate(variable = replace(variable, variable=="V21", "Treatment10")) %>%
mutate(variable = replace(variable, variable=="V22", "Treatment6")) %>%
mutate(variable = replace(variable, variable=="V23", "Treatment10")) %>%
mutate(variable = replace(variable, variable=="V24", "Treatment6")) %>%
mutate(variable = replace(variable, variable=="V25", "Treatment6")) %>%
mutate(variable = replace(variable, variable=="V26", "Treatment10")) %>%
mutate(variable = replace(variable, variable=="V27", "Treatment6")) %>%
mutate(variable = replace(variable, variable=="V28", "Treatment10")) %>%
mutate(Treat = replace(Treat, variable=="Control20", "Control"), Generation = replace(Generation, variable=="Control20", "20")) %>%
mutate(Treat = replace(Treat, variable=="Control6", "Control"), Generation = replace(Generation, variable=="Control6", "6")) %>%
mutate(Treat = replace(Treat, variable=="Control10", "Control"), Generation = replace(Generation, variable=="Control10", "10")) %>%
mutate(Treat= replace(Treat, variable=="Treatment6", "Treatment"), Generation = replace(Generation, variable=="Treatment6", "6")) %>%
mutate(Treat = replace(Treat, variable=="Treatment10", "Treatment"), Generation = replace(Generation, variable=="Treatment10", "10"))
## Adding coverage of each
cov<-select(genoF_cov,3:28)
setDT(cov)
cov<-melt(cov)
MgenoF$Coverage <- cov$value
## Adding which beaker
beaker<-c(rep("BS3C", nrow(genoF)),rep("BS4C", nrow(genoF)),rep("BSE-1", 3*nrow(genoF)), rep("BSE-2", 3*nrow(genoF)), rep("BSE-3", 2*nrow(genoF)), rep("BSE-4", 2*nrow(genoF)),rep("BSE-5", 2*nrow(genoF)), rep("BSE-6", 2*nrow(genoF)),rep("BSE-7", nrow(genoF)),rep("BSE-8", 2*nrow(genoF)),rep("BSE-9", 2*nrow(genoF)),rep("BSE-10", nrow(genoF)),rep("BSE-11", 2*nrow(genoF)),rep("BSE-12", 2*nrow(genoF)))
MgenoF$Beaker<-beaker
## adjust data types and save
MgenoF$Generation <- as.numeric(MgenoF$Generation)
MgenoF$Coverage <- as.numeric(MgenoF$Coverage)
MgenoF$Beaker <- as.factor(MgenoF$Beaker)
MgenoF$Treat <- as.factor(MgenoF$Treat)
MgenoF <- as.data.table(MgenoF)
saveRDS(MgenoF,'hap_blocks.rawAFC.RDS')