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knowledgesystems / signal

Somatic Integration of Germline Alterations in cancer
https://www.signaldb.org/
MIT License
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NaN in GeneTumorTypeFrequencyTable #108

Closed leexgh closed 3 years ago

leexgh commented 3 years ago

NaN in % Biallelic

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Go to: https://www.signaldb.org/explore, then click "+" for "MUTYH"

leexgh commented 3 years ago

This is a data issue. The frequency is from /data/signal.cancertype_specific_somatic_germline_stats.txt, for this case percent_biallelic is NA in file:

Hugo_Symbol penetrance  Proposed_level  num_samples somatic_driver_rate pathogenic_germline_rate    percent_biallelic
MUTYH   Low Small Bowel Cancer  59  0   0.0339  NA

https://github.com/knowledgesystems/signal/blob/master/public/data/signal.cancertype_specific_somatic_germline_stats.txt#L1024

leexgh commented 3 years ago

From Chai:

yes this expected. The "NA" in the "percent_biallelic" column means that we do not have a biallelic status of the pathogenic variant in any of the carriers of that cancer type. The interpretation of this is "Not evaluable". Either leaving the column empty or showing it as '-' would be fine (whatever is consistent with your design practices).