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[Feature request] Add options for BCR clonotype inference #424

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Qile0317 opened this issue Oct 20, 2024 · 0 comments
Open

[Feature request] Add options for BCR clonotype inference #424

Qile0317 opened this issue Oct 20, 2024 · 0 comments
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enhancement New feature or request

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@Qile0317
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Qile0317 commented Oct 20, 2024

I think it may be worthwhile to refactor combineBCR with some new argument like "cloneDefinition" where users can input different methods with the ellipsis argument ... to allow for parameters. While I have no issue with the current definition of clonotypes for BCRs, I can't help but feel it may be better for less technical users to incorporate some of the new methods in the future. There have been quite a few papers just from a quick googlesearch where different methods to cluster BCRs either independently or WITH scRNA data (this can be in a seperate function like inferBCRclonotypes or something) and those can be added.

API wise call.related.clones will be deprecated in favour of something like cloneDefinition="lvCompare" and threshold will be refactored into ... so not a huge change. This chaging process with be eased as well with the newly introduced lifecycle package in #417

Computational speed wise - parseBCR can still be re-done in rcpp I believe since the clonotype inference is done afterwards with lvCompare.

Thoughts? @ncborcherding

@Qile0317 Qile0317 added the enhancement New feature or request label Nov 13, 2024
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