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swaruplabUCI / ArchRtoSignac

An R package performing object conversion from ArchRProject (ArchR) to Signac SeuratObject (Signac)
MIT License
32 stars 11 forks source link

Error with getAnnotation #26

Closed libell1 closed 1 year ago

libell1 commented 1 year ago

Hello,

Thanks for making this code! I am trying to use it, but am running into this error for the annotations:

annotations <- getAnnotation(reference = EnsDb.Hsapiens.v86, refversion = "hg38") # UCSC style [1] "In Progress:" [1] "Extract genomic ranges from EnsDb object and prepare annotation" |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=01m 06s Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE

Any help solving this error would be great, thanks!

rootze commented 1 year ago

@libell1 Thanks for using the ArchRtoSignac package. Please let me know the version of your Signac and Seurat packages. The error you reported may be due to package version of GenomeInfoDb (https://github.com/Bioconductor/GenomeInfoDb/issues/32). It may also be due to other unforeseen circumstances. The new version of Seurat V5 may also have compatible issues with different packages for a while before everything catches up.

libell1 commented 1 year ago

Hi! I have Seurat 4.3.0.1 and Signac 1.10.0 Thanks!

packageVersion("Seurat") [1] '4.3.0.1' packageVersion("Signac") [1] '1.10.0'

rootze commented 1 year ago

@libell1 I hope you have solved the problem. Please let me know if it is due to the package GenomeInfoDb as mentioned above. For now I will close this issue, but feel free to reopen it if needed