#### protein coding
setwd("~/giagkas/RNAseq_POLYseq/")
rp1=read.table("RNA-Poly_0htotal.txt", header = T, sep = "\t")
rp2=read.table("RNA-Poly_2htotal.txt", header = T, sep = "\t")
rp3=read.table("RNA-Poly_6htotal.txt", header = T, sep = "\t")
rp4=read.table("RNA-Poly_IFNtotal.txt", header = T, sep = "\t")
rp5=read.table("RNA-Poly_IL4total.txt", header = T, sep = "\t")

#DEGS protein coding
r1=subset(rp1, (rp1$wtRPKM.RNA>=1)&(rp1$PValue.RNA<0.05)&(abs(rp1$logFC.RNA)>log2(1.5))&(rp1$Biotype=="protein_coding"))
r2=subset(rp2, (rp2$wtRPKM.RNA>=1)&(rp2$PValue.RNA<0.05)&(abs(rp2$logFC.RNA)>log2(1.5))&(rp2$Biotype=="protein_coding"))
r3=subset(rp3, (rp3$wtRPKM.RNA>=1)&(rp3$PValue.RNA<0.05)&(abs(rp3$logFC.RNA)>log2(1.5))&(rp3$Biotype=="protein_coding"))
r4=subset(rp4, (rp4$wtRPKM.RNA>=1)&(rp4$PValue.RNA<0.05)&(abs(rp4$logFC.RNA)>log2(1.5))&(rp4$Biotype=="protein_coding"))
r5=subset(rp5, (rp5$wtRPKM.RNA>=1)&(rp5$PValue.RNA<0.05)&(abs(rp5$logFC.RNA)>log2(1.5))&(rp5$Biotype=="protein_coding"))

p1=subset(rp1, (rp1$wtRPKM.POLY>=1)&(rp1$PValue.POLY<0.05)&(abs(rp1$logFC.POLY)>log2(1.5))&(rp1$Biotype=="protein_coding"))
p2=subset(rp2, (rp2$wtRPKM.POLY>=1)&(rp2$PValue.POLY<0.05)&(abs(rp2$logFC.POLY)>log2(1.5))&(rp2$Biotype=="protein_coding"))
p3=subset(rp3, (rp3$wtRPKM.POLY>=1)&(rp3$PValue.POLY<0.05)&(abs(rp3$logFC.POLY)>log2(1.5))&(rp3$Biotype=="protein_coding"))
p4=subset(rp4, (rp4$wtRPKM.POLY>=1)&(rp4$PValue.POLY<0.05)&(abs(rp4$logFC.POLY)>log2(1.5))&(rp4$Biotype=="protein_coding"))
p5=subset(rp5, (rp5$wtRPKM.POLY>=1)&(rp5$PValue.POLY<0.05)&(abs(rp5$logFC.POLY)>log2(1.5))&(rp5$Biotype=="protein_coding"))


r02=nrow(subset(r1, r2$GeneName%in%r1$GeneName))
r06=nrow(subset(r1, r3$GeneName%in%r1$GeneName))
r0IF=nrow(subset(r1, r4$GeneName%in%r1$GeneName))
r0IL=nrow(subset(r1, r5$GeneName%in%r1$GeneName))
r26=nrow(subset(r2, r3$GeneName%in%r2$GeneName))
r2IF=nrow(subset(r2, r4$GeneName%in%r2$GeneName))
r2IL=nrow(subset(r2, r5$GeneName%in%r2$GeneName))
r6IF=nrow(subset(r3, r4$GeneName%in%r3$GeneName))
r6IL=nrow(subset(r3, r5$GeneName%in%r3$GeneName))
rII=nrow(subset(r4, r5$GeneName%in%r4$GeneName))

p02=nrow(subset(p1, p2$GeneName%in%p1$GeneName))
p06=nrow(subset(p1, p3$GeneName%in%p1$GeneName))
p0IF=nrow(subset(p1, p4$GeneName%in%p1$GeneName))
p0IL=nrow(subset(p1, p5$GeneName%in%p1$GeneName))
p26=nrow(subset(p2, p3$GeneName%in%p2$GeneName))
p2IF=nrow(subset(p2, p4$GeneName%in%p2$GeneName))
p2IL=nrow(subset(p2, p5$GeneName%in%p2$GeneName))
p6IF=nrow(subset(p3, p4$GeneName%in%p3$GeneName))
p6IL=nrow(subset(p3, p5$GeneName%in%p3$GeneName))
pII=nrow(subset(p4, p5$GeneName%in%p4$GeneName))

#RNA DEGs overlaps total
fr1=data.frame(nrow(r1),r02,r06,r0IF,r0IL)
colnames(fr1)=c("0h", "2h", "6h", "IFN", "IL4") 
fr2=data.frame(NA,nrow(r2),r26,r2IF,r2IL)
colnames(fr2)=c("0h", "2h", "6h", "IFN", "IL4") 
fr3=data.frame(NA,NA,nrow(r3),r6IF,r6IL)
colnames(fr3)=c("0h", "2h", "6h", "IFN", "IL4") 
fr4=data.frame(NA,NA,NA,nrow(r4),rII)
colnames(fr4)=c("0h", "2h", "6h", "IFN", "IL4") 
fr5=data.frame(NA,NA,NA,NA,nrow(r5))
colnames(fr5)=c("0h", "2h", "6h", "IFN", "IL4") 

df=rbind(fr1,fr2,fr3,fr4,fr5)
rownames(df)=c("0h", "2h", "6h", "IFN", "IL4") 

setwd("~/giagkas/RNAseq_POLYseq/overlaps/")
write.table(df, file = "overlaps_DEGs_RNAseqPC.txt", quote = F, sep = "\t")


#Polysomes DEGs overlaps total
fp1=data.frame(nrow(p1),p02,p06,p0IF,p0IL)
colnames(fp1)=c("0h", "2h", "6h", "IFN", "IL4") 
fp2=data.frame(NA,nrow(p2),p26,p2IF,p2IL)
colnames(fp2)=c("0h", "2h", "6h", "IFN", "IL4") 
fp3=data.frame(NA,NA,nrow(p3),p6IF,p6IL)
colnames(fp3)=c("0h", "2h", "6h", "IFN", "IL4") 
fp4=data.frame(NA,NA,NA,nrow(p4),pII)
colnames(fp4)=c("0h", "2h", "6h", "IFN", "IL4") 
fp5=data.frame(NA,NA,NA,NA,nrow(p5))
colnames(fp5)=c("0h", "2h", "6h", "IFN", "IL4") 

df=rbind(fp1,fp2,fp3,fp4,fp5)
rownames(df)=c("0h", "2h", "6h", "IFN", "IL4") 

setwd("~/giagkas/RNAseq_POLYseq/overlaps/")
write.table(df, file = "overlaps_DEGs_POLYseqPC.txt", quote = F, sep = "\t")