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LiuzLab / AI_MARRVEL

AI-MARRVEL (AIM) is an AI system for rare genetic disorder diagnosis
GNU General Public License v3.0
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Question about VarTierDiseaseDBFalse.R #23

Closed hyunhwan-bcm closed 2 months ago

hyunhwan-bcm commented 3 months ago
  1. The referred line is flagged IncludeClinVarHGMD, and I believe the intention is not to execute the lines with if(IncludeClinVarHGMD). Is it intentional, or should we pass the parameter to IncludeClinVarHGMD?

https://github.com/LiuzLab/AI_MARRVEL/blob/162ae44442f5cae1cc749fd6740d9fa07c678ab7/run/VarTierDiseaseDBFalse.R#L32

  1. I am confused about the line; just want to make sure that how to treat we are passing the value to VEP.Tier.final properly. Should it be like this?
if ("-" %in% anno$Gene) {
  VEP.Tier.final <- rbind(VEP.Tier.wGene, anno_noGeneID)
} else {
  VEP.Tier.final <- VEP.Tier.wGene
}

https://github.com/LiuzLab/AI_MARRVEL/blob/162ae44442f5cae1cc749fd6740d9fa07c678ab7/run/VarTierDiseaseDBFalse.R#L357-L360