diff --git a/r.scripts/sc-TissueMapper.R b/r.scripts/sc-TissueMapper.R index 0c1d52fc24efd8cb4dfa3b497524ddbfe6b9d6a8..702ab55de12b1573cb071dd7673de1fb3119edbd 100644 --- a/r.scripts/sc-TissueMapper.R +++ b/r.scripts/sc-TissueMapper.R @@ -972,6 +972,7 @@ scTables <- function(sc10x,i.1,i.2){ scDEG <- function(sc10x,i="Lin",g.1="Epi",g.2="St",pct=0.25,t=2){ sc10x <- SetAllIdent(object=sc10x,id=i) genes.deg <- FindMarkers(object=sc10x,ident.1=g.1,ident.2=g.2,min.pct=pct,only.pos=TRUE,thresh.use=0.25,logfc.threshold=log(t)) + genes.deg <- genes.deg[genes.deg$p_val_adj<=0.05,] return(genes.deg) } diff --git a/r.scripts/sc-TissueMapper_RUN.D17.R b/r.scripts/sc-TissueMapper_RUN.D17.R index da6ef490b240da2685c98f2d62064d67911b19fd..1b639cf3b848292c60ee9dfd4bf2307ccd118db9 100644 --- a/r.scripts/sc-TissueMapper_RUN.D17.R +++ b/r.scripts/sc-TissueMapper_RUN.D17.R @@ -280,7 +280,7 @@ genes.deg.LE <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="LE",g.2=c("BE","LE","OE1 genes.deg.OE1 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="OE1",g.2=c("BE","LE","OE2"),pct=0.25,t=2) genes.deg.OE2 <- scDEG(sc10x.Epi.NE,i="Epi.dws.sub",g.1="OE2",g.2=c("BE","LE","OE1"),pct=0.25,t=2) -genes.deg.NE <- scDEG(sc10x.Epi.NE,i="NE",g.1="NE",g.2="ALL",pct=0.25,t=2) +genes.deg.NE <- scDEG(sc10x.Epi.NE,i="NE",g.1="NE",g.2="ALL",pct=0.01,t=1) genes.deg.Fib <- scDEG(sc10x.St,i="Merge_Epi.dws_St.go_NE",g.1="Fib",g.2=c("SM","Endo","Leu"),pct=0.25,t=2) genes.deg.SM <- scDEG(sc10x.St,i="Merge_Epi.dws_St.go_NE",g.1="SM",g.2=c("Fib","Endo","Leu"),pct=0.25,t=2)