f2d118b97ee011247fdc735231bafcc05f1e44ef
kate
  Wed Aug 24 16:09:24 2016 -0700
Tuning GTEx distance and ratio tables for Gene Sorter. refs #17288

diff --git src/hg/near/makeNear.doc src/hg/near/makeNear.doc
index c99333c..c323852 100644
--- src/hg/near/makeNear.doc
+++ src/hg/near/makeNear.doc
@@ -640,34 +640,31 @@
 cd /hive/data/genomes/hg19/bed/gtex
 #hgMapToGene hg19 -type=genePred gtexGeneModelV6 knownGene knownToGtex
 hgMapToGene hg19 -noLoad -all -type=genePred gtexGeneModelV6 knownGene knownToGtex.all
 hgMapToGene hg19 -all -type=genePred gtexGeneModelV6 knownGene knownToGtex
 
 #hgMapToGene hg38 -type=genePred gtexGeneModelV6 knownGene knownToGtex
 hgMapToGene hg38 -all -type=genePred gtexGeneModelV6 knownGene knownToGtex
 
 # Create expression distance table from median table.  This will take about an hour.
 #cd ~/src/hg/near/hgExpDistance
 # TODO: Consider adding weights file
 
 hgsql hgFixed -e select 1.0, id, name from gtexTissue > gtex.weights
 # edit to downweight brain (13 tissues total)
 
-hgExpDistance hg19 -verbose=2 -lookup=knownToGtex \
-        hgFixed.gtexTissueMedian hgFixed.gtexTissue \
-                gtexDistance >&! distance.log &
-
 hgExpDistance hg19 -verbose=2 -lookup=knownToGtex -weights=gtex.weights \
         hgFixed.gtexTissueMedian hgFixed.gtexTissue \
                 gtexDistance2 >&! distance2.log &
 
 # Create ratio table.  
-# TODO: Consider adding -clump file, minAbsVal
-hgRatioMicroarray -database=hgFixed gtexTissueMedian gtexTissueMedianRatio
+# TODO: Consider adding -clump file
+# Defaults for microarray are too high -- RPKM is significant >2 roughly
+hgRatioMicroarray -minAbsVal=2 -minMaxVal=5 -database=hgFixed gtexTissueMedian gtexTissueMedianRatio2
 
 # Get max scores for columnDb.ra
 hgMaxExp hgFixed gtexTissueMedian
 # 219385.91
  
 hgMaxExp hgFixed gtexTissueMedianRatio
 # 12.53