imputeBetas does not work for example EPICv2 data (sesame 1.24.0)

[dwuab]

See the following for details. imputeBetas stopped with the error message that EPICv2.imputationDefault data cannot be found, but I have already run sesameDataCache() successfully. Reruning sesameDataCache() or sesameDataCache("EPICv2.imputationDefault") did not help.

> betas = openSesame(sesameDataGet("EPICv2.8.SigDF")[[1]])
> sum(is.na(betas))
[1] 43946
> betas2 = imputeBetas(betas, "EPICv2")
错误于stopAndCache(title): 
| File EPICv2.imputationDefault either not found or needs to be cached to be
| used in sesame.
| Please make sure you have updated ExperimentHub and try
| > sesameDataCache("EPICv2.imputationDefault")
| or download all data
| > sesameDataCache()
| to retrieve and cache needed sesame data.
> packageVersion("sesame")
[1] ‘1.24.0’

[zwdzwd]

Thank you for bringing this issue to our attention. As you mentioned, imputeBetas stopped due to the missing EPICv2.imputationDefault data, despite successfully running sesameDataCache().

This appears to stem from the current limited public EPICv2 data. We are actively working on assembling an imputation default for EPICv2, which should resolve this issue in the near future.

[zwdzwd]

In the meantime, you might find the following alternative methods that don't require the imputationDefault object helpful:
imputeBetasByGenomicNeighbors: This method imputes beta values using genomic neighbors
imputeBetasMatrixByMean: This approach imputes beta values by taking the mean across samples in a matrix
There are other alternatives such as using nearest neighbor methods, that is currently not implemented in sesame.