The avatar for @lorenasandoval88
lorenasandoval88
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Edited
Jul 23, 2024
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sdk = await import ('https://episphere.github.io/diseasome/sdk.js');
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viewof type = Inputs.select(Object.keys(traitFiles[0]).slice(4), { width: 620, value: "trait_categories", label: "Select by type"})
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pgsVariantsNumber = 40
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viewof disease_ontology_term = Inputs.select(
//efoIds from pgs catalog scoring files only
scoringFilesEfoIds, {value: "EFO:0000712", width: 620, label: "Select by EFO term"})
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pgsIds2 = pgs2.map(x => x.id)
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//in first selection, fixed trait drop down, but synonym breaks sometimes (old version below with map, not flatMap)
// viewof trait = Inputs.select(
// Array.from(new Set( traitFiles.map(x => x[type]).sort().filter(e => e.length).map(JSON.stringify)), JSON.parse)
// , {width: 620, value: "Cancer", label: "Select trait"})
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includesBlanckOntologyTerms = ontologyTerms._embedded.terms.map(x => x.obo_id).sort() // only 1,000 terms out of 4,000
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pgsWithtwoOrMoreEfos = scoringFiles.filter(file=> file.trait_efo.length > 1)
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ontologyTerms = await (await(fetch('https://corsproxy.io/?https://www.ebi.ac.uk/ols/api/ontologies/efo/terms?page=1&size=200'))).json()//await (await(fetchp('https://www.ebi.ac.uk/ols/api/ontologies/efo'))).json()
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scoringFilesEfoIds = [...new Set(scoringFiles.flatMap(x => x.trait_efo.map(y=> {return y.id.replace(/_/g,':')})).sort())]
// ontologyTermsEfoIds = ontologyTerms["_embedded"]["terms"].map(x => x.obo_id).sort()
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tableDataEfo = {
let ids = []
scoringFiles.flatMap((x,i) => x.trait_efo.map(pgs=>{
if(pgs.id===disease_ontology_term.replace(/:/g,'_')){ids.push(x)
}}))
let data = ids.map( o =>
preferredOrder(o,["id","variants_number","trait_reported","name","ftp_scoring_file","ftp_harmonized_scoring_files","publication","matches_publication","samples_variants","samples_training","trait_additional","trait_efo","method_name","method_params", "variants_interactions","variants_genomebuild","weight_type","acestry_distribution",
"date_release","license"])).filter(function (el) {
return el.variants_number <= pgsVariantsNumber
})
if (data.length == 0){
data.push({"id":`no pgs files with less than ${pgsVariantsNumber} SNPs`})
return data
}
return data
}
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