Can't find function AUCell_run

[anemartinezlarrinaga2898]

Hello,

Im trying to run the AUCell library but find this error :

"Can't find the function AUCell_run"

I checked that everything was install and load and it was.

Also by checking with AUCell:: I cannot find the function.

I attached the call to the function:

matrix <- data@assays$RNA@counts
signature.final <- c(signature.x1,signature.x2,signature.x3)
geneSets <- GeneSet(signature.final, setName="Prueba")
cells_AUC <- AUCell_run(matrix, geneSets, aucMaxRank=nrow(cells_rankings)*0.05)

I attached my session info:

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.2.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale:
[1] es_ES.UTF-8/es_ES.UTF-8/es_ES.UTF-8/C/es_ES.UTF-8/es_ES.UTF-8

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] AUCell_1.16.0        GSEABase_1.56.0      graph_1.72.0         annotate_1.72.0      XML_3.99-0.10        AnnotationDbi_1.56.2 IRanges_2.28.0      
 [8] S4Vectors_0.32.4     Biobase_2.54.0       BiocGenerics_0.40.0  sp_1.5-0             SeuratObject_4.1.0  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3                lattice_0.20-45             listenv_0.8.0               png_0.1-7                   Biostrings_2.62.0          
 [6] digest_0.6.29               parallelly_1.32.0           mime_0.12                   R6_2.5.1                    GenomeInfoDb_1.30.1        
[11] RSQLite_2.2.14              httr_1.4.3                  zlibbioc_1.40.0             rlang_1.0.3                 rstudioapi_0.13            
[16] data.table_1.14.2           blob_1.2.3                  R.oo_1.25.0                 R.utils_2.12.0              Matrix_1.4-1               
[21] stringr_1.4.0               RCurl_1.98-1.7              bit_4.0.4                   DelayedArray_0.20.0         shiny_1.7.1                
[26] compiler_4.1.3              httpuv_1.6.5                globals_0.15.1              rgeos_0.5-9                 htmltools_0.5.2            
[31] SummarizedExperiment_1.24.0 KEGGREST_1.34.0             GenomeInfoDbData_1.2.7      progressr_0.10.1            matrixStats_0.62.0         
[36] codetools_0.2-18            future_1.26.1               crayon_1.5.1                later_1.3.0                 bitops_1.0-7               
[41] R.methodsS3_1.8.2           grid_4.1.3                  xtable_1.8-4                lifecycle_1.0.1             DBI_1.1.3                  
[46] magrittr_2.0.3              future.apply_1.9.0          cli_3.3.0                   stringi_1.7.6               cachem_1.0.6               
[51] XVector_0.34.0              promises_1.2.0.1            ellipsis_0.3.2              vctrs_0.4.1                 tools_4.1.3                
[56] bit64_4.0.5                 MatrixGenerics_1.6.0        parallel_4.1.3              fastmap_1.1.0               GenomicRanges_1.46.1       
[61] memoise_2.0.1

Thanks in advanced : )

[xychen24]

I have the same problem!

[anemartinezlarrinaga2898]

I solved it!

Instead of running the function AUCell_run you have to run it in two different steps:

cell.ranking <- AUCell_buildRankings(exprMat = matrix.filtrada.interes,nCores = 4)
AuCell.Signature.1 <- AUCell_calcAUC(geneSets = gene.set.1,
                                     rankings =cell.ranking,
                                     nCores = 4,
                                     aucMaxRank = ceiling(0.05 * nrow(cell.ranking)))

Is the same as running AUCell_run, it is specify in the tutorial but you need to read it carefully to see it : )

[xychen24]

Thanks a lot! I will try this way!

[s-aibar]

Hello, Thank you for reporting this issue. However, this problem should be solved in newer versions of AUCell. Please, update the package, and let us know if the problem persists.

Also note that a new version will be published in a couple of weeks (on Nov. 2), with the latest version of Bioconductor.