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cumc / xqtl-protocol

Molecular QTL analysis protocol developed by ADSP Functional Genomics Consortium
https://cumc.github.io/xqtl-protocol/
MIT License
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TensorQTL indices possible bug #998

Closed minqiao closed 2 weeks ago

minqiao commented 3 months ago

When submitting jobs using TensorQTL.ipynb, there is either KeyError or ValueError. I changed the following indices

    pairs_df.columns.values[7]  = "pvalue"
    pairs_df.columns.values[8]  = "beta"
    pairs_df.columns.values[9]  = "se"

to

    pairs_df.columns.values[6]  = "pvalue"
    pairs_df.columns.values[7]  = "beta"
    pairs_df.columns.values[8]  = "se"

in [cis_1], it went through smoothly without raising errors.

gaow commented 3 months ago

Thanks @minqiao . @grennfp could you take a look and verify it on your end with some test data and fix it as necessary? @Bale4 this has to do with the sQTL bug?