31:Te5a,pgs.Match3=async(data, progressReport)=>{ // extract harmonized data from PGS entry first const indChr = data.pgs.cols.indexOf('hm_chr') const indPos = data.pgs.cols.indexOf('hm_pos') // match let dtMatch = [] const cgrInd = data.pgs.cols.indexOf('hm_chr') const posInd = data.pgs.cols.indexOf('hm_pos') const n = data.pgs.dt.length //progressCalc.hidden = false let i = 0 let j = 0 //index of last match, the nex can match will have to be beyond this point since both pgs and 23and me are sorted by chr/position //let matchFloor=0 // to advance the earliest match as it advances function funMatch(i = 0, matchFloor = 0) { if (i < n) { let r = data.pgs.dt[i] // PGS data to be matched if (dtMatch.length > 0) { matchFloor = dtMatch.at(-1)[0][4] } // MATCH 23andme chromosome and position TO PGS chromosome and position ******* // also filter by pgs alt or effect allele match var regexPattern = new RegExp([r[2],r[3]].join('|')) let dtMatch_i = data.my23.dt.filter(myr => (myr[2] == r[indPos])). filter(myr => (myr[1] == r[indChr])). filter(myr => regexPattern.test(myr[3]))//also filter by pgs alt or effect allele match console.log(regexPattern) console.log("pgs",r[3]) console.log("pgs",r[2]) console.log("23",data.my23.dt[i][3]) console.log("match--------", regexPattern.test(data.my23.dt[i][3]))//data.my23.dt[i][3]).match(/G/g)) if (dtMatch_i.length > 0) { dtMatch.push(dtMatch_i.concat([r])) } setTimeout(() => { funMatch(i + 1) }, 0) } else { let calcRiskScore = [] let aleles = [] data.pgsMatchMy23 = dtMatch // calculate Risk let logR = 0 // log(0)=1 let ind_effect_allele = data.pgs.cols.indexOf('effect_allele') let ind_other_allele = data.pgs.cols.indexOf('other_allele') let ind_effect_weight = data.pgs.cols.indexOf('effect_weight') let ind_allelefrequency_effect = data.pgs.cols.indexOf('allelefrequency_effect') dtMatch.forEach((m, i) => { calcRiskScore[i] = 0 // default no risk aleles[i] = 0 // default no alele let mi = m[0][3].match(/^[ACGT]{2}$/) // we'll only consider duplets in the 23adme report if (mi) { //'effect_allele', 'other_allele', 'effect_weight' mi = mi[0] // 23andme match let pi = m.at(-1) //pgs match let alele = pi[ind_effect_allele] let L = mi.match(RegExp(alele, 'g')) // how many, 0,1, or 2 if (L) { L = L.length calcRiskScore[i] = L * pi[ind_effect_weight] aleles[i] = L } } }) data.aleles = aleles data.calcRiskScore = calcRiskScore if (calcRiskScore.reduce((a, b) => Math.min(a, b)) == 0) { //&&(calcRiskScore.reduce((a,b)=>Math.max(a,b))<=1)){ // hazard ratios? console.log('these are not betas :-(') } else { data.PRS = Math.exp(calcRiskScore.reduce((a, b) => a + b)) } } } funMatch() return data }32:[{"id":"700b48c52a2bf94d9f4589fb8300446669eef9f32bc2f7264ff26e8ddf83d91cb199b0517eb6e1186364bd682c056f2e42b61b7087f6e2a0d99bba03045987fd","href":"https://static.observableusercontent.com/files/700b48c52a2bf94d9f4589fb8300446669eef9f32bc2f7264ff26e8ddf83d91cb199b0517eb6e1186364bd682c056f2e42b61b7087f6e2a0d99bba03045987fd","name":"genome_Chad_Wrye_v5_Full_20220921063742.txt","type":"text/plain","lastModified":1674771084028.799,"size":16648209},{"id":"3f333484c29d56926b18b1e6c86320da0cc8a84edddaa6fad79c57b2ecd0b85e0b8eaefcc386b022709e01d16e8968f71ac518edbf7bfe0c1a9f27e5b7cb36d4","href":"https://static.observableusercontent.com/files/3f333484c29d56926b18b1e6c86320da0cc8a84edddaa6fad79c57b2ecd0b85e0b8eaefcc386b022709e01d16e8968f71ac518edbf7bfe0c1a9f27e5b7cb36d4","name":"genome_Dorothy_Wolf_v4_Full_20170525101345.txt","type":"text/plain","lastModified":1674771084028.799,"size":15702997},{"id":"216249139aa0fee9e5f841c9602f434348a68935f277553c863c5d4da207f9f4c419f49fff27b10c07f998355e449f3881de6611dc7258268cb166f905843298","href":"https://static.observableusercontent.com/files/216249139aa0fee9e5f841c9602f434348a68935f277553c863c5d4da207f9f4c419f49fff27b10c07f998355e449f3881de6611dc7258268cb166f905843298","name":"image.png","type":"image/png","lastModified":1674852298101.385,"size":14606},{"id":"15b6f70953f06a534e604aef70152908b3620b9fd8c52de73aaf53ff4f2a87096c4ac01c2133cd730a6d9b0ec8f750da94e22dd02a75c0db8a3a41a2e42a5400","href":"https://static.observableusercontent.com/files/15b6f70953f06a534e604aef70152908b3620b9fd8c52de73aaf53ff4f2a87096c4ac01c2133cd730a6d9b0ec8f750da94e22dd02a75c0db8a3a41a2e42a5400","name":"image@1.png","type":"image/png","lastModified":1674852355694.163,"size":10725}] 2f:{"title":"","cells":[{"id":0,"value":"md`## Polygenic Risk Score (PRS) Calc\n\n\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":112,"value":"md`Calculation of polygenic risk scores from the PGS catalog to inform the cumulative effect of an individual's genetic risk for some disease or trait
`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1002,"value":"md`### Step 1: Load genomic data\nLoad 23 and me file or select on from dropdown list`","pinned":false,"hidden":false,"mode":"ojs"},{"id":504,"value":"viewof pgs23 = Inputs.file({label: \"load your 23andme file\",accept: \".json,.txt\", required: false})","pinned":false,"hidden":false,"mode":"ojs"},{"id":560,"value":"viewof pgs23dropDown = Inputs.select([null].concat(Object.keys(genomeList)), {required: true,value:\"none selected\",label: \"or choose preloaded male or female files\"})","pinned":false,"hidden":false,"mode":"ojs"},{"id":2052,"value":"{if (pgs23dropDown== \"none selected\" & pgs23== null){\n var file = \"please load or select file from drop down\"\n return file\n}}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1558,"value":"File loaded: ${prs23.info} (${prs23.dt.length} variants)","pinned":false,"hidden":false,"mode":"html"},{"id":1629,"value":"md`\n\n---\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":48,"value":"md`### Step 2: load catalog entry\nEdit PGS entry id below to generate a new result:`","pinned":false,"hidden":false,"mode":"ojs"},{"id":52,"value":"id = \"PGS000001\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":1607,"value":"Study of ${pgsAttr.variants_number} variants associated with ${pgsAttr.trait_reported}","pinned":false,"hidden":false,"mode":"html"},{"id":1639,"value":"PGSdiv = DOM.element(\"div\");","pinned":false,"hidden":false,"mode":"ojs"},{"id":1547,"value":"md`\n\n---\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1007,"value":"md`### Step 3: calculate Polygenic Risk Scores`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1733,"value":"riskdiv = DOM.element(\"div\");\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":1364,"value":"div2 = DOM.element(\"div\");\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":1791,"value":"piediv = DOM.element(\"div\")","pinned":false,"hidden":false,"mode":"ojs"},{"id":1319,"value":"data = Promises.delay(23000,results)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1633,"value":"md`\n\n---\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":469,"value":"md`## 23andme SNP file`","pinned":false,"hidden":false,"mode":"ojs"},{"id":610,"value":"prs23 = {\n var dt23 = \"choose file from drop down or load your own\" \n // no file loaded or chose from dropdown\n if(pgs23dropDown==undefined && pgs23==undefined){\n var dt23 = \"choose file from drop down or load your own\"\n \n } else if(pgs23dropDown!=undefined && pgs23==undefined ){\n var dt23 = pgs.parse23(genomeList[pgs23dropDown],pgs23dropDown)\n\n } else if(pgs23dropDown==undefined && pgs23!=undefined){\n var text23 = await pgs23.text()\n var dt23 = pgs.parse23(text23,pgs23.name)\n \n } else if(pgs23dropDown==\"none selected\" && pgs23!=undefined ){\n var text23 = await pgs23.text()\n var dt23 = pgs.parse23(text23,pgs23.name)\n } else if(pgs23dropDown!=undefined && pgs23!=undefined ){\n var dt23 = pgs.parse23(genomeList[pgs23dropDown],pgs23dropDown)\n\n } \nreturn dt23\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":961,"value":"prs23_textArea = pgs.prs23textArea((prs23.txt).substring(0,5000))","pinned":true,"hidden":false,"mode":"ojs"},{"id":44,"value":"md`## ${pgsAttr.id} scoring file`","pinned":false,"hidden":false,"mode":"ojs"},{"id":75,"value":"txt = pgs.textArea(id)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1034,"value":"prsPGS = pgs.parsePGS(id)","pinned":false,"hidden":false,"mode":"ojs"},{"id":142,"value":"md` PGS entry attributes, values, and individual snp rsid `","pinned":false,"hidden":false,"mode":"ojs"},{"id":130,"value":"pgsAttr = pgs.get(`score/${id}?format=json`) // pgs.info","pinned":false,"hidden":false,"mode":"ojs"},{"id":765,"value":"md`## Functions`","pinned":false,"hidden":false,"mode":"ojs"},{"id":1596,"value":"import {textcolor} from \"@observablehq/text-color-annotations-in-markdown\"","pinned":false,"hidden":false,"mode":"ojs"},{"id":1452,"value":"math = require('https://cdnjs.cloudflare.com/ajax/libs/mathjs/1.5.2/math.min.js')","pinned":false,"hidden":false,"mode":"ojs"},{"id":1138,"value":"Plotly = require(\"https://cdn.plot.ly/plotly-latest.min.js\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":13,"value":"pgs = require(\"https://episphere.github.io/prs/pgs.js\")","pinned":true,"hidden":false,"mode":"ojs"},{"id":694,"value":"genomeList = ({\"none selected\":\"none selected\", \"genome_Chad_Wrye_v5_Full_20220921063742.txt\":await FileAttachment(\"genome_Chad_Wrye_v5_Full_20220921063742.txt\").text(), \"genome_Dorothy_Wolf_v4_Full_20170525101345.txt\": await FileAttachment(\"genome_Dorothy_Wolf_v4_Full_20170525101345.txt\").text()})","pinned":false,"hidden":false,"mode":"ojs"},{"id":1386,"value":"{div2.innerHTML = \"loading effect size plot...please wait\"\ndiv2.style = \"color:red;font-size =15\"\nreturn div2}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1016,"value":"results={\n const obj1={\"my23\":prs23}\n const obj2={\"pgs\":prsPGS}\n\n const dt = Object.assign(obj1,obj2)\n let res = pgs.Match2(dt)\n\nreturn res\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1495,"value":"pgs.plotAllMatchByPos(data,div2)","pinned":true,"hidden":false,"mode":"ojs"},{"id":1754,"value":"reloadScore = {if (results.calcRiskScore==undefined){\n riskdiv.innerHTML = `loading risk score...`;\n}\n}","pinned":false,"hidden":false,"mode":"ojs"},{"id":1667,"value":"riskScore={\n pgs23dropDown;\n\n let data2 = data\n if (data2.calcRiskScore==undefined){\n riskdiv.innerHTML = `loading risk score...\"`;\n }\n else {\n riskdiv.innerHTML =`Risk score for ${data.pgsMatchMy23.length}/${data.pgs.dt.length} \"${data.pgs.meta.trait_reported}\" variants found in genomic file = \n ${math.round(math.exp( math.sum(data2.calcRiskScore)),3)}`;\n }\n return riskdiv\n}\n","pinned":false,"hidden":false,"mode":"ojs"},{"id":1526,"value":"pgs.pgsPlot(prsPGS,PGSdiv)","pinned":false,"hidden":false,"mode":"ojs"},{"id":1921,"value":"//betas = data.pgsMatchMy23.map(function(b) {return parseFloat( b[1][4])});\n//data.betas = (betas)\n// prs = math.sum(Array(data.betas.length).fill(0).map((_, i) => data.betas[i]*data.aleles[i] ))","pinned":true,"hidden":false,"mode":"ojs"},{"id":1998,"value":"$31","pinned":false,"hidden":false,"mode":"ojs"},{"id":1784,"value":"pie = pgs.piechart(data,piediv)","pinned":false,"hidden":false,"mode":"ojs"}],"files":"$W32","stdlib":"1","titling":"auto"}