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Hi there.
I think Sarek is in a good place with the current ASCAT implementation, but I'd like to point towards two things that I think would be helpful for the community.
The function ascat.aspcf() (found in the ascat module) accepts a parameter penalty which controls the sensitivity of the tool to potential segment breakpoints. The default is 70 which is usually fine, but for individuals using panel/wes data being able to change this value might be helpful - any chance of exposing this as a param?
The function ascat.aspcf() (found in the ascat module) accepts a parameter penalty which controls the sensitivity of the tool to potential segment breakpoints. The default is 70 which is usually fine, but for individuals using panel/wes data being able to change this value might be helpful - any chance of exposing this as a param?
This seems easy enough, I'm fairly sure we can add that for 3.5.0
I split your initial issue in 2 different feature requests
maxulysse
changed the title
Copy-Number Enhancements - ascat_penality
Copy-Number Enhancements - Ascat penality
May 7, 2024
Description of feature
Hi there.
I think Sarek is in a good place with the current ASCAT implementation, but I'd like to point towards two things that I think would be helpful for the community.
ascat.aspcf()
(found in the ascat module) accepts a parameterpenalty
which controls the sensitivity of the tool to potential segment breakpoints. The default is 70 which is usually fine, but for individuals using panel/wes data being able to change this value might be helpful - any chance of exposing this as aparam
?Kind regards,
George
EDIT by @maxulysse - created #1512
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