navinlabcode / navinlabcode/CellTrek
Error: invalid character indexing
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Description
Hi,
I am running celltrek with default settings, but I am encountering the following error, I am not able to debug, please let me know if this can be resolved. Thanks a lot
`s21_h8_celltrek <- CellTrek::celltrek(st_sc_int=ct_train, int_assay='traint', sc_data=sc, sc_assay = 'RNA',
reduction='pca', intp=T, intp_pnt=5000, intp_lin=F, nPCs=30, ntree=1000,
dist_thresh=0.55, top_spot=5, spot_n=5, repel_r=20, repel_iter=20, keep_model=T)$celltrek`
`09:18:32 Optimization finished
Rasterizing points since number of points exceeds 100,000.
To disable this behavior set `raster=FALSE`
Joining, by = c("Var1", "Var2", "value", "val_rsc", "Var1_type", "Var2_type")
Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE) :
invalid character indexing
Calls: <Anonymous> ... callGeneric -> eval -> eval -> [ -> [ -> subCsp_cols -> intI
Execution halted.
Regards,
AMK
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First steps
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Research direction
Start by reproducing the reported CellTrek::celltrek call with the shown defaults and inspect the traceback at subCsp_cols/intI after the rasterization and join messages. Determine which character index is invalid for this input; done means the same call completes without the error, with a regression check for the case.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100