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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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hlaAssocTest() #16

Closed mukhtarsadykov closed 2 years ago

mukhtarsadykov commented 2 years ago

Dear Xiuwen,

I am doing association test between disease and hla. When I run the hlaAssocTest(), i am getting the following message: "Warning in hlaAssocTest.hlaAlleleClass(hla, disease ~ h, data = df_short) : glm does not work."

I found that HLA types are from 2015. Could it be the problem that some of my hlas are not in the database of this package? Would it be right if I just add the new updated HLAs to HIBAG/extdata/v3.22.0/hla_nom_g.txt ? Do you know what could be the reason why glm doesn't work?

thank you!

mukhtarsadykov commented 2 years ago

Resolved. The problem was with the format of one of my columns, it was a character while the glm requires numeric/integer.