84 lines
2.5 KiB
Go
84 lines
2.5 KiB
Go
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package polygenicDiseases
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import "seekia/internal/helpers"
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import _ "embed"
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import "errors"
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import "encoding/gob"
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import "bytes"
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import "maps"
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//go:embed rsIDs/GiantObesityStudyLoci.gob
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var GiantObesityStudyLociFile []byte
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func getObesityDiseaseObject()(PolygenicDisease, error){
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// Map Structure: rsID -> References Map
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locusReferencesMap := make(map[int64]map[string]string)
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referencesMap_List1 := make(map[string]string)
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referencesMap_List1["GIANT consortium - Meta-analyses of Genome-Wide Association Studies - 2022 - Obesity"] = "https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files"
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// These SNPs are taken from the meta-analyses of Genome-Wide Association Studies (GWAS) created by the GIANT consortium
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//https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files
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// Download link:
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// https://portals.broadinstitute.org/collaboration/giant/images/0/09/PublicRelease.WHRadjBMI.C.All.Add.txt.gz
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// SHA-256 Checksum:
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// 2a863b0357037ae5c34853342052ed3c59735d6440da0fd15d1cab34b7d49daf
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// See /utilities/extractGiantLoci/extractGiantLoci.go to see how they were extracted from the file
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buffer := bytes.NewBuffer(GiantObesityStudyLociFile)
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decoder := gob.NewDecoder(buffer)
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var lociList_1 []int64
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err := decoder.Decode(&lociList_1)
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if (err != nil){ return PolygenicDisease{}, err }
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for _, rsID := range lociList_1{
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locusReferencesMap[rsID] = maps.Clone(referencesMap_List1)
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}
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obesityLociList := helpers.GetListOfMapKeys(locusReferencesMap)
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referencesMap := make(map[string]string)
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referencesMap["Obesity Genome-Wide Association Study (GWAS) created by the GIANT consortium"] = "https://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files"
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getAverageRiskProbabilitiesFunction := func(maleOrFemale string, inputAge int)(float64, error){
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// Roughly 30% of people are obese.
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if (maleOrFemale == "Male"){
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return 0.30, nil
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}
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if (maleOrFemale != "Female"){
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return 0, errors.New("Trying to get breast cancer risk probability for invalid maleOrFemale: " + maleOrFemale)
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}
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//TODO: Add different probabilities per age
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return 0.30, nil
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}
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obesityObject := PolygenicDisease{
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DiseaseName: "Obesity",
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EffectedSex: "Both",
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DiseaseDescription: "The condition of having an excessive amount of body fat.",
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LocusReferencesMap: locusReferencesMap,
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LociList: obesityLociList,
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GetAverageRiskProbabilitiesFunction: getAverageRiskProbabilitiesFunction,
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References: referencesMap,
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}
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return obesityObject, nil
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}
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