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morinlab / GAMBLR

Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
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Implement flatfile functionality for CNV and introduce cnvKompare #86

Closed Kdreval closed 2 years ago

Kdreval commented 2 years ago

This PR introduces the flatfile functionality for CNV to avoid reliance on the database. The useful feature here is a new cnvKompare function that will compare CNV data for patients with multiple time points and calculate the overall concordance of CNV + other comparison data. It can also handle the comparison of CNV between different tools if needed.

Kdreval commented 2 years ago

This also addresses and resolves issue #19

Kdreval commented 2 years ago

Thanks for review Laura! I fixed these issues, and also added additional function to specify minimum similarity between cytobands to be considered concordant/discordant