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" )