Bug report: Running scROSHI returnError in data.frame(barcodes = names(ct.annot), cell.type = as.character(ct.annot),: arguments imply differing number of rows

[JohannesGawron]

We I tried running the function scROSHI I get the above error.

Here's the exact command I ran:

scROSHI(sce_data = sce,
        celltype_lists = marker_list,
        type_config = config,
        gene_symbol = 'X',
        count_data = 'dsb_no_iso',
        verbose = 1
        )

My singleCellExperiment objects looks like this:

class: SingleCellExperiment 
dim: 45 3769 
metadata(2): libraryName assayMetadata
assays(5): counts clrc clrb dsb dsb_no_iso
rownames: NULL
rowData names(1): X
colnames: NULL
colData names(2): Sample Cell_Barcode
reducedDimNames(1): PCA
mainExpName: NULL
altExpNames(0):

R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.3.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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

time zone: Europe/Zurich
tzcode source: internal

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

other attached packages:
 [1] scROSHI_1.0.0.0             umap_0.2.10.0               SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2 Biobase_2.60.0              GenomicRanges_1.52.1        GenomeInfoDb_1.36.4        
 [8] IRanges_2.34.1              S4Vectors_0.38.2            BiocGenerics_0.46.0         MatrixGenerics_1.12.3       matrixStats_1.2.0           rhdf5_2.44.0                lubridate_1.9.3            
[15] forcats_1.0.0               stringr_1.5.1               dplyr_1.1.4                 purrr_1.0.2                 readr_2.1.5                 tidyr_1.3.1                 tibble_3.2.1               
[22] ggplot2_3.5.0               tidyverse_2.0.0             Rcpp_1.0.12                

loaded via a namespace (and not attached):
 [1] gtable_0.3.4            xfun_0.42               lattice_0.21-8          tzdb_0.4.0              rhdf5filters_1.12.1     vctrs_0.6.5             tools_4.3.1             bitops_1.0-7            generics_0.1.3         
[10] parallel_4.3.1          fansi_1.0.6             pkgconfig_2.0.3         Matrix_1.6-5            lifecycle_1.0.4         GenomeInfoDbData_1.2.10 FNN_1.1.4               compiler_4.3.1          farver_2.1.1           
[19] munsell_0.5.0           htmltools_0.5.7         RCurl_1.98-1.14         yaml_2.3.8              pillar_1.9.0            crayon_1.5.2            uwot_0.1.16             openssl_2.1.1           limma_3.56.2           
[28] DelayedArray_0.26.7     abind_1.4-5             RSpectra_0.16-1         tidyselect_1.2.0        digest_0.6.34           stringi_1.8.3           labeling_0.4.3          fastmap_1.1.1           grid_4.3.1             
[37] colorspace_2.1-0        cli_3.6.2               magrittr_2.0.3          S4Arrays_1.0.6          utf8_1.2.4              withr_3.0.0             scales_1.3.0            bit64_4.0.5             timechange_0.3.0       
[46] rmarkdown_2.26          XVector_0.40.0          igraph_2.0.2            bit_4.0.5               reticulate_1.35.0       png_0.1-8               askpass_1.2.0           hms_1.1.3               evaluate_0.23          
[55] knitr_1.45              irlba_2.3.5.1           rlang_1.1.3             glue_1.7.0              pkgload_1.3.4           jsonlite_1.8.8          rstudioapi_0.15.0       vroom_1.6.5             R6_2.5.1               
[64] Rhdf5lib_1.22.1         zlibbioc_1.46.0

[JohannesGawron]

It seems the issue is in the function f_score_ctgenes_U:
The line colnames(mat) <- sce$barcodes assumes that the colData of the input singleCellExperiment-object has a column named "barcodes".
May I suggest to either state this in the documentation, or to enable the user to pass an argument that specifies the name of the barcodes-column?

Also, it would be nice to have a more verbose error output.

Thanks a lot and best,
Johannes