Comments (4)
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.
from cellula.
> 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 ```
from cellula.
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!
from cellula.
This worked with the following:
sce = assignIdentities(sce, genesets = plasma_genes, method = "UCell", name = "UCell_plasma")
Thanks
from cellula.
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