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Commit ce0cff61 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Add table for raw cell #'s for FACS pops

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r.scripts/sc_Tables.R
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...@@ -40,4 +40,5 @@ if (!dir.exists(paste0("./analysis/",opt$g,"/global/table"))){ ...@@ -40,4 +40,5 @@ if (!dir.exists(paste0("./analysis/",opt$g,"/global/table"))){
write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],file=paste0("./analysis/",opt$g,"/global/table/Table.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",") write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],file=paste0("./analysis/",opt$g,"/global/table/Table.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",") write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[5:6,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.ALLSubPop+NE.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
write.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[1:4,],file=paste0("./analysis/",opt$g,"/global/table/Table.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[1:4,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",") write.table(round(prop.table(table(sc10x.Group@meta.data$samples,sc10x.Group@meta.data$'ALLSubPop+NE')[1:4,],1)*100,1),file=paste0("./analysis/",opt$g,"/global/table/ProbTable.FACS.csv"),row.names=TRUE,col.names=NA,append=FALSE,sep=",")
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