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Commit 5989f0d2 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Change St cell type DEGs to generate compared to St

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with 18 additions and 9 deletions
r.scripts/sc_DEG.R
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......@@ -107,6 +107,15 @@ DEG.Fib.vs.SM <- DEG.Fib.vs.SM[DEG.Fib.vs.SM$p_val_adj<0.05,]
DEG.SM.vs.Fib <- FindMarkers(object=sc10x.Group.NoStress,ident.1=unique(as.character(sc10x.Group.NoStress@ident)[grep("^SM",as.character(sc10x.Group.NoStress@ident))]),ident.2=unique(as.character(sc10x.Group.NoStress@ident)[grep("^Fib",as.character(sc10x.Group.NoStress@ident))]),min.pct=0.25,only.pos=TRUE,thresh.use=0.25,logfc.threshold=log(2))
DEG.SM.vs.Fib <- DEG.SM.vs.Fib[DEG.SM.vs.Fib$p_val_adj<0.05,]
DEG.Endo.vs.St <- FindMarkers(object=sc10x.Group.NoStress,ident.1=unique(as.character(sc10x.Group.NoStress@ident)[grep("^Endo",as.character(sc10x.Group.NoStress@ident))]),ident.2=c(unique(as.character(sc10x.Group.NoStress@ident)[grep("^Fib",as.character(sc10x.Group.NoStress@ident))]),unique(as.character(sc10x.Group.NoStress@ident)[grep("^SM",as.character(sc10x.Group.NoStress@ident))]),unique(as.character(sc10x.Group.NoStress@ident)[grep("^Leu",as.character(sc10x.Group.NoStress@ident))])),min.pct=0.25,only.pos=TRUE,thresh.use=0.25,logfc.threshold=log(2))
DEG.Endo.vs.St <- DEG.Endo.vs.St[DEG.Endo.vs.St$p_val_adj<0.05,]
DEG.Fib.vs.St <- FindMarkers(object=sc10x.Group.NoStress,ident.1=unique(as.character(sc10x.Group.NoStress@ident)[grep("^Fib",as.character(sc10x.Group.NoStress@ident))]),ident.2=c(unique(as.character(sc10x.Group.NoStress@ident)[grep("^Endo",as.character(sc10x.Group.NoStress@ident))]),unique(as.character(sc10x.Group.NoStress@ident)[grep("^SM",as.character(sc10x.Group.NoStress@ident))]),unique(as.character(sc10x.Group.NoStress@ident)[grep("^Leu",as.character(sc10x.Group.NoStress@ident))])),min.pct=0.25,only.pos=TRUE,thresh.use=0.25,logfc.threshold=log(2))
DEG.Fib.vs.St <- DEG.Fib.vs.St[DEG.Fib.vs.St$p_val_adj<0.05,]
DEG.SM.vs.St <- FindMarkers(object=sc10x.Group.NoStress,ident.1=unique(as.character(sc10x.Group.NoStress@ident)[grep("^SM",as.character(sc10x.Group.NoStress@ident))]),ident.2=c(unique(as.character(sc10x.Group.NoStress@ident)[grep("^Fib",as.character(sc10x.Group.NoStress@ident))]),unique(as.character(sc10x.Group.NoStress@ident)[grep("^Endo",as.character(sc10x.Group.NoStress@ident))]),unique(as.character(sc10x.Group.NoStress@ident)[grep("^Leu",as.character(sc10x.Group.NoStress@ident))])),min.pct=0.25,only.pos=TRUE,thresh.use=0.25,logfc.threshold=log(2))
DEG.SM.vs.St <- DEG.SM.vs.St[DEG.SM.vs.St$p_val_adj<0.05,]
DEG.Leu.vs.St <- FindMarkers(object=sc10x.Group.NoStress,ident.1=unique(as.character(sc10x.Group.NoStress@ident)[grep("^Leu",as.character(sc10x.Group.NoStress@ident))]),ident.2=c(unique(as.character(sc10x.Group.NoStress@ident)[grep("^Fib",as.character(sc10x.Group.NoStress@ident))]),unique(as.character(sc10x.Group.NoStress@ident)[grep("^SM",as.character(sc10x.Group.NoStress@ident))]),unique(as.character(sc10x.Group.NoStress@ident)[grep("^Endo",as.character(sc10x.Group.NoStress@ident))])),min.pct=0.25,only.pos=TRUE,thresh.use=0.25,logfc.threshold=log(2))
DEG.Leu.vs.St <- DEG.Leu.vs.St[DEG.Leu.vs.St$p_val_adj<0.05,]
DEG.Leu.vs.EpiSt <- FindMarkers(object=sc10x.Group.NoStress,ident.1=unique(as.character(sc10x.Group.NoStress@ident)[grep("^Leu",as.character(sc10x.Group.NoStress@ident))]),ident.2=c(unique(as.character(sc10x.Group.NoStress@ident)[grep("^BE",as.character(sc10x.Group.NoStress@ident))]),unique(as.character(sc10x.Group.NoStress@ident)[grep("^LE",as.character(sc10x.Group.NoStress@ident))]),"OE1","OE2",unique(as.character(sc10x.Group.NoStress@ident)[grep("^Fiv",as.character(sc10x.Group.NoStress@ident))]),unique(as.character(sc10x.Group.NoStress@ident)[grep("^SM",as.character(sc10x.Group.NoStress@ident))])),min.pct=0.25,only.pos=TRUE,thresh.use=0.25,logfc.threshold=log(2))
DEG.Leu.vs.EpiSt <- DEG.Leu.vs.EpiSt[DEG.Leu.vs.EpiSt$p_val_adj<0.05,]
......@@ -183,17 +192,17 @@ dev.off()
if (opt$ne==FALSE){
DEG.NE.vs.Epi <- ""
}
DEG_BE <- setdiff(rownames(DEG.BE.vs.Epi),Reduce(union,list(rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.SM),rownames(DEG.SM.vs.Fib),rownames(DEG.Endo.vs.FMSt),rownames(DEG.Leu.vs.EpiSt))))
DEG_LE <- setdiff(rownames(DEG.LE.vs.Epi),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.SM),rownames(DEG.SM.vs.Fib),rownames(DEG.Endo.vs.FMSt),rownames(DEG.Leu.vs.EpiSt))))
DEG_OE1 <- setdiff(rownames(DEG.OE1.vs.Epi),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.SM),rownames(DEG.SM.vs.Fib),rownames(DEG.Endo.vs.FMSt),rownames(DEG.Leu.vs.EpiSt))))
DEG_OE2 <- setdiff(rownames(DEG.OE2.vs.Epi),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.SM),rownames(DEG.SM.vs.Fib),rownames(DEG.Endo.vs.FMSt),rownames(DEG.Leu.vs.EpiSt))))
DEG_BE <- setdiff(rownames(DEG.BE.vs.Epi),Reduce(union,list(rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.St),rownames(DEG.SM.vs.St),rownames(DEG.Endo.vs.St),rownames(DEG.Leu.vs.St))))
DEG_LE <- setdiff(rownames(DEG.LE.vs.Epi),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.St),rownames(DEG.SM.vs.St),rownames(DEG.Endo.vs.St),rownames(DEG.Leu.vs.St))))
DEG_OE1 <- setdiff(rownames(DEG.OE1.vs.Epi),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.St),rownames(DEG.SM.vs.St),rownames(DEG.Endo.vs.St),rownames(DEG.Leu.vs.St))))
DEG_OE2 <- setdiff(rownames(DEG.OE2.vs.Epi),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.St),rownames(DEG.SM.vs.St),rownames(DEG.Endo.vs.St),rownames(DEG.Leu.vs.St))))
if (opt$ne==TRUE){
DEG_NE <- setdiff(rownames(DEG.NE.vs.Epi),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.Fib.vs.SM),rownames(DEG.SM.vs.Fib),rownames(DEG.Endo.vs.FMSt),rownames(DEG.Leu.vs.EpiSt))))
DEG_NE <- setdiff(rownames(DEG.NE.vs.Epi),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.Fib.vs.St),rownames(DEG.SM.vs.St),rownames(DEG.Endo.vs.St),rownames(DEG.Leu.vs.St))))
}
DEG_Fib <- setdiff(rownames(DEG.Fib.vs.SM),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.SM.vs.Fib),rownames(DEG.Endo.vs.FMSt),rownames(DEG.Leu.vs.EpiSt))))
DEG_SM <- setdiff(rownames(DEG.SM.vs.Fib),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.SM),rownames(DEG.Endo.vs.FMSt),rownames(DEG.Leu.vs.EpiSt))))
DEG_Endo <- setdiff(rownames(DEG.Endo.vs.FMSt),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.SM),rownames(DEG.SM.vs.Fib),rownames(DEG.Leu.vs.EpiSt))))
DEG_Leu <- setdiff(rownames(DEG.Leu.vs.EpiSt),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.SM),rownames(DEG.SM.vs.Fib),rownames(DEG.Endo.vs.FMSt))))
DEG_Fib <- setdiff(rownames(DEG.Fib.vs.St),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.SM.vs.St),rownames(DEG.Endo.vs.St),rownames(DEG.Leu.vs.St))))
DEG_SM <- setdiff(rownames(DEG.SM.vs.St),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.St),rownames(DEG.Endo.vs.St),rownames(DEG.Leu.vs.St))))
DEG_Endo <- setdiff(rownames(DEG.Endo.vs.St),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.St),rownames(DEG.SM.vs.St),rownames(DEG.Leu.vs.St))))
DEG_Leu <- setdiff(rownames(DEG.Leu.vs.St),Reduce(union,list(rownames(DEG.BE.vs.Epi),rownames(DEG.LE.vs.Epi),rownames(DEG.OE1.vs.Epi),rownames(DEG.OE2.vs.Epi),rownames(DEG.NE.vs.Epi),rownames(DEG.Fib.vs.St),rownames(DEG.SM.vs.St),rownames(DEG.Endo.vs.St))))
if (opt$ne==TRUE){
DEG <- c(DEG_BE[1:5],DEG_LE[1:5],DEG_OE1[1:5],DEG_OE2[1:5],DEG_NE[1:5],DEG_Fib[1:5],DEG_SM[1:5],DEG_Endo[1:5],DEG_Leu[1:5])
} else {
......
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