Commit 266a45c8 authored by Gervaise H. Henry's avatar Gervaise H. Henry 🤠

Remove unnecesary rownames from PdPgb diy degs

parent 1722636e
......@@ -8,29 +8,31 @@
#SBATCH --mail-type ALL
#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
git pull origin Seurat3.0
rm ../analysis/*.rda
rm ../analysis/*.RData
rm -r ../analysis/cor/
rm -r ../analysis/qc/
rm -r ../analysis/score_id/
rm -r ../analysis/shiny/
rm -r ../analysis/vis/
#git pull origin Seurat3.0
#rm ../analysis/*.rda
#rm ../analysis/*.RData
#rm -r ../analysis/cor/
#rm -r ../analysis/qc/
#rm -r ../analysis/score_id/
#rm -r ../analysis/shiny/
#rm -r ../analysis/vis/
module load python/3.6.4-anaconda
source activate umap
module load R/3.5.1-gccmkl
module load hdf5_18/1.8.17
Rscript ../r.scripts/sc-TissueMapper_RUN.R --p "$1" --s "$2"
#Rscript ../r.scripts/sc-TissueMapper_RUN.R --p "$1" --s "$2"
module unload R/3.5.1-gccmkl
module load R/3.6.1-gccmkl
if [[ "$1" == "PdPgb" ]] || [[ "$1" == "PdPb" ]]
then
Rscript ../r.scripts/SingleR.R --p "$1" --s "$2" --o "$3"
# Rscript ../r.scripts/SingleR.R --p "$1" --s "$2" --o "$3"
echo 1
elif [ "$3" == "epi" || "$3" == "fmst" ]
then
Rscript ../r.scripts/huPr_muPr.R --p "$1" --r "$3"
# Rscript ../r.scripts/huPr_muPr.R --p "$1" --r "$3"
echo 2
fi
module unload R/3.5.1-gccmkl
......
......@@ -219,5 +219,5 @@ for (i in c("BE","LE","Hillock","Club","NE","Fib","SM")){
data <- subset(sc10x,idents=i)
Idents(data) <- "Phenotype"
deg <- FindAllMarkers(data,assay="SCT",slot="data",logfc.threshold=0,test.use="MAST")
write.table(deg,file=paste0("./analysis/vis/diy/DEG_pheno.",i,".csv"),sep=",",quote=FALSE,row.names=TRUE,col.names=NA)
write.table(deg,file=paste0("./analysis/vis/diy/DEG_pheno.",i,".csv"),sep=",",quote=FALSE,row.names=FALSE,col.names=TRUE)
}
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