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zhengxwen / HIBAG

R package – HLA Genotype Imputation with Attribute Bagging (development version only)
https://hibag.s3.amazonaws.com/index.html
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HLA prediction quality #11

Open rcanovas opened 4 years ago

rcanovas commented 4 years ago

Is there any way to obtain the quality (r2 or INFO) of imputing HLA-* ? So far, after doing the prediction I can only see the alleles and only one probability.

zhengxwen commented 4 years ago

Use that probability for a pair of alleles, and a threshold 0.5. Or output all prob. of the full pairs of alleles,

hlaPredict(object, snp, type="prob")