When using assigning identities, some cell annotation labels are missing for the UCell method about cellula

[gdagstn]

Hi Cathal, thanks for reporting.

Would you mind checking how the geneset intersects with the rownames of your object?

Something like:

lapply(genesets, function(x) table(x %in% rownames(sce)))

where genesets is the list containing the Hay bone marrow sets.

[cathalgking]

> str(result)
List of 700
 $ AIZARANI_LIVER_C1_NK_NKT_CELLS_1                                          : 'table' int [1(1d)] 195
  ..- attr(*, "dimnames")=List of 1
  .. ..$ : chr "TRUE"
 $ AIZARANI_LIVER_C10_MVECS_1                                                : 'table' int [1:2(1d)] 6 287
  ..- attr(*, "dimnames")=List of 1
  .. ..$ : chr [1:2] "FALSE" "TRUE"
 $ AIZARANI_LIVER_C11_HEPATOCYTES_1                                          : 'table' int [1:2(1d)] 3 327
  ..- attr(*, "dimnames")=List of 1
  .. ..$ : chr [1:2] "FALSE" "TRUE"
 $ AIZARANI_LIVER_C12_NK_NKT_CELLS_4                                         : 'table' int [1(1d)] 59
  ..- attr(*, "dimnames")=List of 1
  .. ..$ : chr "TRUE"
 $ AIZARANI_LIVER_C13_LSECS_2                                                : 'table' int [1:2(1d)] 9 301
  ..- attr(*, "dimnames")=List of 1
  .. ..$ : chr [1:2] "FALSE" "TRUE"`

$AIZARANI_LIVER_C1_NK_NKT_CELLS_1

TRUE 
 195 

$AIZARANI_LIVER_C10_MVECS_1

FALSE  TRUE 
    6   287 

$AIZARANI_LIVER_C11_HEPATOCYTES_1

FALSE  TRUE 
    3   327 

$AIZARANI_LIVER_C12_NK_NKT_CELLS_4

TRUE 
  59 

$AIZARANI_LIVER_C13_LSECS_2

FALSE  TRUE 
    9   301 

$AIZARANI_LIVER_C14_HEPATOCYTES_2

FALSE  TRUE 
    2   263 ```

[gdagstn]

ok it sounds like there aren't many genes missing for every signature - I'd say you can proceed as usual. if you see very weird results let me know!

[cathalgking]

This worked with the following:
sce = assignIdentities(sce, genesets = plasma_genes, method = "UCell", name = "UCell_plasma")
Thanks