Add annotation of point mutations in create gene binary pipeline

Question

Add annotation of point mutations in create gene binary pipeline

Opened this issue a year ago · 3 comments

We can require this as a preprocessing step, or add an arg in create_gene_binary(). We will think on it more and maybe ask Caroline and Alli for preference.

Maybe we want to do fuzzy matching to throw warnings when their selected mutation doesn't exist.

Answer 1 · 2023-09-21T15:30:28.000Z

@hfuchs5 to get test data for this and maybe assign to someone else.

Explore adding an argument to create_gene_binary() to filter and add an event column for a specific point mutation (if found in their file). If not found, throw message.

Answer 2 · 2023-11-09T16:12:55.000Z

https://atlasgeneticsoncology.org/teaching/30067/nomenclature-for-the-description-of-mutations-and-other-sequence-variations

Answer 3 · 2023-12-14T18:33:33.000Z

Notes:

Make sure periods in hugo symbol/ point mutation name are handled correctly (eg. does it conflict with .fus, .Del etc)
Make sure the hugo symbol is identifiable within point mutation column name
perhaps make them name them "PM etc."