ShixiangWang / sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html
https://shixiangwang.github.io/sigminer/
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get_sig_similarity only goes up to COSMIC_30 #415

Closed maia-munteanu closed 2 years ago

maia-munteanu commented 2 years ago

Perhaps this is due to the v3.3 update to COSMIC, but now using the get_sig_similarity function only provides cosine similarity results for the first 30 SBS signatures, thus excluding the other ones and providing skewed results.

As an example:

Input matrix (96 rows, standard SBS96 format) Screenshot from 2022-08-29 17-13-57

Function output Screenshot from 2022-08-29 17-13-20

Content of similarity results Screenshot from 2022-08-29 17-18-34

Thanks, Maia

ShixiangWang commented 2 years ago

@maia-munteanu Maia, please read doc at https://shixiangwang.github.io/sigminer/reference/get_sig_similarity.html.

You can change the sig_db to "SBS". You can also download the latest data from cosmic and provide it as a reference.

maia-munteanu commented 2 years ago

Ah, thank you so much! I must've been using this option previously and forgot to add it again.

Maia