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steverozen / mSigHdp

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Using custom catalog categories #8

Open mandronescu opened 3 hours ago

mandronescu commented 3 hours ago

Hello,

Thank you for a very useful package!

I would like to use your code to run HDP mutational signatures on custom catalog categories (for example I just want to use 10 categories instead of 96 that are in SBS96). I can see how this is done in the original Roberts' hdp code, but I can't find how to do it in mSigHdp/hdpx, it seems like the catalog types are already fixed in ICAMS.

Can you please advise?

Thank you! Mirela.

mandronescu commented 2 hours ago

Hi again, I am able to run mSigHdp if I give as input.catalog a matrix, obtained with data.matrix(myinput).

It would be good though to be able to add my custom categories as an ICAMS type, so I can better benefit from plotting. Thanks!

liumoLM commented 1 minute ago

Hi Mirela,

mSigHdp relies on the ICAMS functions for its visualization. A simpler workaround is to expand your 10 categories into 96, filling the remaining 86 categories with zeros. This approach should not impact the extraction process.

Feel free to let me know if you have any questions.

Thanks, Mo

On Fri, 20 Sept 2024 at 06:16, mandronescu @.***> wrote:

Hi again, I am able to run mSigHdp if a give as input.catalog a matrix, obtained with data.matrix(myinput). Thanks!

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