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Commit 75c4e6ce authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add DEG generation to ds.D17

parent 1399756b
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r.scripts/sc-TissueMapper_RUN.DS_D17.R
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......@@ -345,6 +345,42 @@ rm(i)
rm(g)
genes.deg.Stress <- scDEG(sc10x.Stress,i="Stress",g.1="Stress",g.2="ALL",pct=0.5,t=5)
genes.deg.Epi <- scDEG(sc10x,i="Lin",g.1="Epi",g.2="St",t=2)
genes.deg.St <- scDEG(sc10x,i="Lin",g.1="St",g.2="Epi",t=2)
genes.deg.BE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sc",g.1="BE",g.2=c("LE","OE_SCGB","OE_KRT13"),pct=0.25,t=2)
genes.deg.LE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sc",g.1="LE",g.2=c("BE","LE","OE_SCGB","OE_KRT13"),pct=0.25,t=2)
genes.deg.OE1 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sc",g.1="OE_SCGB",g.2=c("BE","LE","OE_KRT13"),pct=0.25,t=2)
genes.deg.OE2 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sc",g.1="OE_KRT13",g.2=c("BE","LE","OE_SCGB"),pct=0.25,t=2)
genes.deg.NE <- scDEG(sc10x.Epi.NE,i="NE",g.1="NE",g.2=c("BE","LE","OE_KRT13","OE_SCGB","sample"),pct=0.01,t=1)
genes.deg.Fib <- scDEG(sc10x.St,i="Merge_Epi.dws.sc_St.dws.sc",g.1="Fib",g.2=c("SM","Endo","Leu"),pct=0.25,t=2)
genes.deg.SM <- scDEG(sc10x.St,i="Merge_Epi.dws.sc_St.dws.sc",g.1="SM",g.2=c("Fib","Endo","Leu"),pct=0.25,t=2)
genes.deg.Endo <- scDEG(sc10x.St,i="Merge_Epi.dws.sc_St.dws.sc",g.1="Endo",g.2=c("Fib","SM","Leu"),pct=0.25,t=2)
genes.deg.Leu <- scDEG(sc10x.St,i="St.dws.sc",g.1="Leu",g.2=c("Fib","SM","Endo"),pct=0.25,t=2)
genes.deg.BE.unique <- setdiff(rownames(genes.deg.BE),Reduce(union,list(rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.LE.unique <- setdiff(rownames(genes.deg.LE),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.OE1.unique <- setdiff(rownames(genes.deg.OE1),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.OE2.unique <- setdiff(rownames(genes.deg.OE2),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.NE.unique <- setdiff(rownames(genes.deg.NE),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.Fib.unique <- setdiff(rownames(genes.deg.Fib),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.SM),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.SM.unique <- setdiff(rownames(genes.deg.SM),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.Endo),rownames(genes.deg.Leu))))
genes.deg.Endo.unique <- setdiff(rownames(genes.deg.Endo),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Leu))))
genes.deg.Leu.unique <- setdiff(rownames(genes.deg.Leu),Reduce(union,list(rownames(genes.deg.BE),rownames(genes.deg.LE),rownames(genes.deg.OE1),rownames(genes.deg.OE2),rownames(genes.deg.NE),rownames(genes.deg.Fib),rownames(genes.deg.SM),rownames(genes.deg.Endo))))
genes.deg.5 <- c(genes.deg.BE.unique[1:5],genes.deg.LE.unique[1:5],genes.deg.OE1.unique[1:5],genes.deg.OE2.unique[1:5],genes.deg.NE.unique[1:5],genes.deg.Fib.unique[1:5],genes.deg.SM.unique[1:5],genes.deg.Endo.unique[1:5],genes.deg.Leu.unique[1:5])
genes.deg.5 <- rev(genes.deg.5)
genes.deg.10 <- c(genes.deg.BE.unique[1:10],genes.deg.LE.unique[1:10],genes.deg.OE1.unique[1:10],genes.deg.OE2.unique[1:10],genes.deg.NE.unique[1:10],genes.deg.Fib.unique[1:10],genes.deg.SM.unique[1:10],genes.deg.Endo.unique[1:10],genes.deg.Leu.unique[1:10])
genes.deg.10 <- rev(genes.deg.10)
for (i in ls(pattern="^genes.deg")){
write.table(get(i),file=paste0("./analysis/deg/",i,".csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
}
save(list=ls(pattern="sc10x.Stress"),file="./analysis/sc10x.Stress.Rda")
rm(list=ls(pattern="sc10x.Stress"))
save(list=ls(pattern="sc10x.Epi"),file="./analysis/sc10x.Epi.Rda")
......
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