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carmonalab / ProjecTILs

Interpretation of cell states using reference single-cell maps
GNU General Public License v3.0
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BiocParallel errors #44

Closed gianfilippo closed 1 year ago

gianfilippo commented 1 year ago

Hi,

I am testing your package on my mouse data.

I loaded my data in a Seurat object and did some basic filtering

I then loaded the mouse TILs reference and then run the make.projection function seuratOBJ.proj = make.projection(seuratOBJ, ref = reference, ncores = 20, query.assay = "RNA", scGate_model="mouse")

Below is the output, including errors. what is strange is also that one run worked and a rerun, right after it, with the exact same command and data, fails as below Can you please help me with this ? Thanks

[1] "Using assay RNA for WT_INJ" Pre-filtering cells with scGate...

[1] "Using assay RNA for WT" Pre-filtering cells with scGate...

[1] "Using assay RNA for TFGA" Pre-filtering cells with scGate...

[1] "Using assay RNA for E18.5" Pre-filtering cells with scGate...

Error: BiocParallel errors 4 remote errors, element index: 1, 2, 3, 4 0 unevaluated and other errors first remote error: Error in dplyr::distinct(., .data$name, .data$signature, .keep_all = T): Must use existing variables.

gianfilippo commented 1 year ago

Hi,

I am obviously making a stupid mistake. I set scGate_model="mouse", when it should have been a proper model (as specified by scGate).

Best