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Thanks for making a great tool!
In v1.1, the nominal and permute output is inconsistent when there are no local variants.
In nominal mode, the gene ids will simply be missing from the output. In permute mode, the gene ids will be included in the output, but with NA for the values.
Including such gene ids in the nominal output (but with NA for values) would facilitate a quick check for users to make sure output was generated for all input genes.
Best,
--Leland
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