Add files via upload

hanjunlee21 · Feb 9, 2022 · 4b9c4df · 4b9c4df
1 parent 265fe34
commit 4b9c4df
Show file tree

Hide file tree

Showing 4 changed files with 1,264 additions and 0 deletions.
diff --git a/ComponentAnalysis/ComponentAnalysis_sim.sh b/ComponentAnalysis/ComponentAnalysis_sim.sh
@@ -0,0 +1,22 @@
+R="NORMAL"
+Q="DLBCL"
+O="DLBCLvsNORMAL"
+PYTHONVERSION="python3.7"
+
+# backup
+cp ~/miniconda3/lib/$PYTHONVERSION/site-packages/chess/sim.py sim_backup.py
+
+# inverse of Fano factor ("SN")
+chess sim -p 4 ../COOL/$R.chr2.25kb.KR.cool ../COOL/$Q.chr2.25kb.KR.cool ../Pairs/hg19.chr2.2Mb.500kb.txt ../CHESS/chr2.2Mb.500kb/$O.tsv
+
+# foldchange
+cp sim_foldchange.py ~/miniconda3/lib/$PYTHONVERSION/site-packages/chess/sim.py
+chess sim -p 4 ../COOL/$R.chr2.25kb.KR.cool ../COOL/$Q.chr2.25kb.KR.cool ../Pairs/hg19.chr2.2Mb.500kb.txt ../CHESS/chr2.2Mb.500kb/$O.foldchange.tsv
+
+# variance
+cp sim_variance.py ~/miniconda3/lib/$PYTHONVERSION/site-packages/chess/sim.py
+chess sim -p 4 ../COOL/$R.chr2.25kb.KR.cool ../COOL/$Q.chr2.25kb.KR.cool ../Pairs/hg19.chr2.2Mb.500kb.txt ../CHESS/chr2.2Mb.500kb/$O.variance.tsv
+
+# recovery
+cp sim_backup.py ~/miniconda3/lib/$PYTHONVERSION/site-packages/chess/sim.py
+