007a3bff22438077c95cf425e22877644704c23a
kate
  Tue Sep 15 15:25:10 2020 -0700
1. Size lollies based on #studies. 2. Display p-value in E notation (request from Juha). refs #26129

diff --git src/hg/makeDb/outside/covid/covidHgiGwas.as src/hg/makeDb/outside/covid/covidHgiGwas.as
index 63f0a2a..b3bea60 100644
--- src/hg/makeDb/outside/covid/covidHgiGwas.as
+++ src/hg/makeDb/outside/covid/covidHgiGwas.as
@@ -1,23 +1,25 @@
 table covidHgiGwas
-"Meta-analysis from COVID 19 Host Genetics Initiative (covid19hg.org).  BED 9+10 for lollipop display"
+"Meta-analysis from COVID 19 Host Genetics Initiative (covid19hg.org).  BED 9+12 for lollipop display"
     (
     string   chrom;            "Reference sequence chromosome or scaffold"
     uint     chromStart;       "Start position in chrom"
     uint     chromEnd;         "End position in chrom"
     string   name;             "dbSNP Reference SNP (rs) identifier or <chromNum>:<pos>"
     uint     score;            "Score from 0-1000, derived from p-value"
     char[1]  strand;           "Unused.  Always '.'"
     uint     thickStart;       "Start position in chrom"
     uint     thickEnd;         "End position in chrom"
     uint     color;            "Red (positive effect) or blue (negative). Brightness reflects pvalue"
-    double   effectSize;       "Effect size on log(OR) scale
+    double   effectSize;       "Effect size (beta coefficient)
     double   effectSizeSE;     "Effect size standard error"
-    double   pValue;           "-log10 p-value"
-    double   pValueHet;        "-log10 p-value from Cochran's Q heterogeneity test"
+    string   pValue;           "p-value"
+    double   pValueLog;        "-log10 p-value"
+    string   pValueHet;        "p-value from Cochran's Q heterogeneity test"
     lstring  ref;              "Non-effect allele"
     lstring  alt;              "Effect allele"
     double   alleleFreq;       "Allele frequency among the samples"
     uint     sampleN;          "Total sample size (sum of study sample sizes)"
     uint     sourceCount;      "Number of studies"
-    double   _effectSizeAbs;   "Effect size on log(OR) scale, abs value for display"
+    uint     _radius;          "Lollipop radius; scaled ratio of sourceCount to total studies, for display"
+    double   _effectSizeAbs;   "Effect size, abs value for display"
     )