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ErasmusMC-CCBC / katdetectr

An R package for detection, characterization and visualization of kataegis.
GNU General Public License v3.0
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Annotation of variant types #5

Closed ekaterina-akimova closed 9 months ago

ekaterina-akimova commented 9 months ago

Hello,

I have recently re-analyzed some data using katdetectr package and compared it to the previous analysis with maftools. Hereby I noticed, that katdetectr reinfallplot function summarizes all indels and all A>C, A>G, A>T, G>A, G>C, G>T as "Others", which is confusing, because, to my knowledge, normally the A>C, A>G, A>T, G>A, G>C, G>T variant counts are added up to their complement equivalents C>A,C>G,C>T,T>A,T>C,T>G. I'm curious, if there is a specific reason for this desicion? It is of course possible to modify the input data to get the plots as I want them. However, if there is an explanation, may be biological relevance, I am not aware of, I would reconsider my analysis.

I'd be happy to hear from you! Thank you!

daanhazelaar commented 9 months ago

Hi @ekaterina-akimova,

Thank you for pointing this out! Indeed, we mistakenly labelled the substitutions: G>A, G>C, G>T, A>G, A>T and A>C as "other" instead of labelling them as their complement equivalents according to the standard pyrimidine classification of single nucleotide variants (SNV).

Please note that indels or other variants that are not SNVs are labelled as "other" in the rainfallplot constructed by katdetectr. Additionally, katdetectr merges overlapping variants (for example two substitutions with the exact same position) into a single record. These merged records are also labelled as "other".

I have just pushed an update to include the correct labelling in the rainfallplot of katdetectr. Please let me know if you have any more comments or recommendations regarding katdetectr!

# download the latest version of katdetectr from github
if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")
devtools::install_git(url = "https://github.com/ErasmusMC-CCBC/katdetectr")
ekaterina-akimova commented 9 months ago

Hello @daanhazelaar,

thank you for such a rush response and an update! I tested the new version (1.5.1) on my data set just now and it worked nicely.

Best,