auto_detect_tissue_type error

[antoine4ucsd]

Hello thank you for making this package available. really needed!

I am having trouble with the auto_detect functionn

auto_detect_tissue_type(path_to_db_file = db_, seuratObject = myseurat object, scaled = F,
+                                        assay = "RNA") 

and I got the following error after several min

Checking...Immune system"
Selecting by scores
[1] "Checking...Pancreas"
Selecting by scores
[1] "Checking...Liver"
Selecting by scores
[1] "Checking...Eye"
Selecting by scores
[1] "Checking...Kidney"
Selecting by scores
[1] "Checking...Brain"
Selecting by scores
[1] "Checking...Lung"
Selecting by scores
[1] "Checking...Adrenal"
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'args' in selecting a method for function 'do.call': error in evaluating the argument 'x' in selecting a method for function 'head': arguments imply differing number of rows: 1, 0
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Called from: h(simpleError(msg, call))

and the warnings

Browse[1]> warnings()
Warning messages:
1: In checkGeneSymbols(markers_all) :
  Human gene symbols should be all upper-case except for the 'orf' in open reading frames. The case of some letters was corrected.
2: In checkGeneSymbols(markers_all) : x contains non-approved gene symbols
3: In checkGeneSymbols(markers_all) : x contains non-approved gene symbols
4: In checkGeneSymbols(markers_all) : x contains non-approved gene symbols
5: In checkGeneSymbols(markers_all) : x contains non-approved gene symbols
6: In checkGeneSymbols(markers_all) : x contains non-approved gene symbols
7: In checkGeneSymbols(markers_all) : x contains non-approved gene symbols
8: In checkGeneSymbols(markers_all) : x contains non-approved gene symbols
9: In checkGeneSymbols(markers_all) : x contains non-approved gene symbols
10: In checkGeneSymbols(markers_all) : x contains non-approved gene symbols
11: In checkGeneSymbols(markers_all) : x contains non-approved gene symbols
12: In checkGeneSymbols(markers_all) : x contains non-approved gene symbols

Any thoughts?

thank you!

[IanevskiAleksandr]

Dear @antoine4ucsd ,

We've made updates to the _auto_detect_tissuetype function, and it should be working as intended now. If you still encounter issues, please don't hesitate to reopen the comment thread.

BR, Aleksandr

[antoine4ucsd]

Great news. I will give it a try. thank you for letting me know and for continuing improving this package.