Error in Aggregate.Formula

[hraeder41]

Hello,

When I attempt to run JaBbA after the gGraph has already been created:

`JaBbA 2024-03-04 14:59:47: Number of gaps with nonzero width: 5558
JaBbA 2024-03-04 14:59:47: Number of segments before gap filtering: 8337
JaBbA 2024-03-04 14:59:48: 2779 segments produced after gap filtering
JaBbA 2024-03-04 14:59:48: creating karyograph
JaBbA 2024-03-04 15:00:14: Definining coverage good quality nodes as >=50% bases covered by non-NA and non-Inf values in +/-100KB region
JaBbA 2024-03-04 15:00:14: Hard setting 0 Mb of the genome to NA that didn't pass our quality threshold
JaBbA 2024-03-04 15:00:14: Using loess to fit mean to variance relationship in segments with greater than 1 bins
JaBbA 2024-03-04 15:00:14: Using ppgrid to estimate purity ploidy
JaBbA 2024-03-04 15:00:14: setting up ppgrid matrices ..

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JaBbA 2024-03-04 15:00:16: Built gGraph with 5826 nodes, 412 edges, purity 0.78, and ploidy 1.23
Error in aggregate.formula(...) : 'formula' missing or incorrect
Calls: suppressPackageStartupMessages ... vaggregate -> aggregate -> aggregate -> aggregate.formula`

Everything appears to run correctly before this, and there do not appear to be any issues when loading my junction or coverage files. Do you have any insight into what may be causing this error?

[jrafailov]

Hi Henry,

It's likely an R versioning issue as the base aggregate function changed in R 4.2+. Can you please try with R 4.1.3 or R 4.0.2?

[hraeder41]

Thank you for the quick response! I was actually able to avoid this by providing a purity and ploidy estimate. If that seems incorrect, please let me know. Thank you again!

[hraeder41]

Actually, as an update here, I have found that the key is that JaBbA always succeeds the second time I attempt to run it on a sample (i.e. I get the aggregate error the first time, and when I rerun it I do not). Do you have any ideas on why this may occur? Thank you!

[jrafailov]

Hi, it's likely you are using an outdated gTrack package when running JaBbA. You are getting the aggregate error the first time because the karyograph is generated in that run and your error likely occurs in plotting the karyograph gTrack. In the second run, since your karyograph was already generated, JaBbA is passing over that code.

Please see commit 4aa01d0 of gTrack, which addresses this error.