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tf2 / CNest

Copy Number Methods for Detection and Genome Wide Association Tests
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Merging calls #11

Open nandobonf opened 2 years ago

nandobonf commented 2 years ago

Hi, I read with great interest the paper on Cell Genomics and I was wondering if you can also provide a script to generate the merged copy number events (CNVEs) as described in the paper for better reproducibility. Thanks!

nandobonf commented 1 year ago

@tf2 any update on this? Thank you!

tf2 commented 1 year ago

yep - many apologies for the slow reply - on it... you will notice there is a R package push just now in the "src" dir called "recipeB" -- please try and install that as a first step... there is a function called "rbreak" which is very flexible and can do the merging you require. I will provide example of how it works when you let me know its installed ok (it requires a few parameters to be set and a speific input format)....

nandobonf commented 1 year ago

thanks and apologies for my late reply (I missed somehow the notification). However, I'm still not able to make it work, i get many warnings in R. I will post you later the logs. Thanks!