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morinlab / GAMBLR

Set of standardized functions to operate with genomic data
MIT License
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get_sample_cn_segments has non-standard parameter naming #224

Closed rdmorin closed 11 months ago

rdmorin commented 1 year ago

The recent update to get_sample_cn_segments adds a "multiple_samples" parameter and an optional "sample_list", which together allow the user to provide more than one sample_id. The standard implementation we've used in other GAMBLR functions is:

these_sample_ids (a vector of length >=1 of sample_id the user wants returned)

The function should be able to figure out, based on the length of that vector, if the user wants one or more samples returned. I don't understand why the function was updated this way instead. Also why aren't you making use of the new id_ease and a these_samples_metadata argument?

mattssca commented 1 year ago

Thanks for posting this issue. I agree, this function should be updated to deal with sample IDs in the same way as other GAMBLR functions do. I will do an overhaul of this function and update it accordingly. Side note, the git blame shows that the non-standard arguments were introduced last year.