Unable to find an inherited method for function ‘bg’ for signature ‘"PFMatrix"’

[alkurowska]

I am trying to covert my PFMatrixList into PWMatrixList

toPWM(my_PFMatrixList)

And I get the following error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘bg’ for signature ‘"PFMatrix"’

> sessionInfo()
R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Rocky Linux 9.1 (Blue Onyx)

Matrix products: default
BLAS/LAPACK: /home/kurowsaa/miniconda3/envs/chromVAR_env/lib/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Asia/Riyadh
tzcode source: system (glibc)

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

other attached packages:
 [1] BiocManager_1.30.22               lubridate_1.9.3                  
 [3] forcats_1.0.0                     stringr_1.5.1                    
 [5] dplyr_1.1.4                       purrr_1.0.2                      
 [7] readr_2.1.5                       tidyr_1.3.1                      
 [9] tibble_3.2.1                      ggplot2_3.5.0                    
[11] tidyverse_2.0.0                   BSgenome.Hsapiens.UCSC.hg38_1.4.5
[13] BSgenome_1.70.1                   rtracklayer_1.62.0               
[15] BiocIO_1.12.0                     Biostrings_2.70.1                
[17] XVector_0.42.0                    GenomicRanges_1.54.1             
[19] GenomeInfoDb_1.38.1               IRanges_2.36.0                   
[21] S4Vectors_0.40.2                  BiocGenerics_0.48.1              
[23] TFBSTools_1.40.0                  chromVAR_1.24.0                  
[25] motifmatchr_1.24.0                ComplexHeatmap_2.18.0            
[27] learnMotifs_0.1.0                

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          jsonlite_1.8.8             
  [3] shape_1.4.6.1               magrittr_2.0.3             
  [5] GlobalOptions_0.1.2         zlibbioc_1.48.0            
  [7] vctrs_0.6.5                 memoise_2.0.1              
  [9] Rsamtools_2.18.0            RCurl_1.98-1.14            
 [11] base64enc_0.1-3             htmltools_0.5.8            
 [13] S4Arrays_1.2.0              CNEr_1.38.0                
 [15] SparseArray_1.2.2           pracma_2.4.4               
 [17] htmlwidgets_1.6.4           plyr_1.8.9                 
 [19] plotly_4.10.4               cachem_1.0.8               
 [21] GenomicAlignments_1.38.0    whisker_0.4.1              
 [23] mime_0.12                   lifecycle_1.0.4            
 [25] iterators_1.0.14            pkgconfig_2.0.3            
 [27] Matrix_1.6-5                R6_2.5.1                   
 [29] fastmap_1.1.1               GenomeInfoDbData_1.2.11    
 [31] MatrixGenerics_1.14.0       shiny_1.8.1                
 [33] clue_0.3-65                 digest_0.6.35              
 [35] colorspace_2.1-0            TFMPvalue_0.0.9            
 [37] AnnotationDbi_1.64.1        RSQLite_2.3.4              
 [39] seqLogo_1.68.0              timechange_0.3.0           
 [41] fansi_1.0.6                 tfruns_1.5.2               
 [43] httr_1.4.7                  abind_1.4-5                
 [45] compiler_4.3.3              withr_3.0.0                
 [47] bit64_4.0.5                 doParallel_1.0.17          
 [49] BiocParallel_1.36.0         DBI_1.2.2                  
 [51] R.utils_2.12.3              tensorflow_2.15.0          
 [53] poweRlaw_0.80.0             DelayedArray_0.28.0        
 [55] rjson_0.2.21                gtools_3.9.5               
 [57] caTools_1.18.2              tools_4.3.3                
 [59] httpuv_1.6.15               ggseqlogo_0.2              
 [61] R.oo_1.26.0                 glue_1.7.0                 
 [63] restfulr_0.0.15             promises_1.2.1             
 [65] keras_2.13.0                cluster_2.1.6              
 [67] reshape2_1.4.4              generics_0.1.3             
 [69] gtable_0.3.4                tzdb_0.4.0                 
 [71] R.methodsS3_1.8.2           data.table_1.15.2          
 [73] hms_1.1.3                   utf8_1.2.4                 
 [75] ggrepel_0.9.5               foreach_1.5.2              
 [77] pillar_1.9.0                later_1.3.2                
 [79] circlize_0.4.16             lattice_0.22-6             
 [81] bit_4.0.5                   annotate_1.80.0            
 [83] tidyselect_1.2.1            DirichletMultinomial_1.44.0
 [85] GO.db_3.18.0                miniUI_0.1.1.1             
 [87] SummarizedExperiment_1.32.0 Biobase_2.62.0             
 [89] matrixStats_1.2.0           DT_0.32                    
 [91] stringi_1.8.3               lazyeval_0.2.2             
 [93] yaml_2.3.8                  codetools_0.2-19           
 [95] cli_3.6.2                   xtable_1.8-4               
 [97] reticulate_1.35.0           munsell_0.5.0              
 [99] Rcpp_1.0.12                 zeallot_0.1.0              
[101] png_0.1-8                   XML_3.99-0.16.1            
[103] parallel_4.3.3              blob_1.2.4                 
[105] bitops_1.0-7                viridisLite_0.4.2          
[107] scales_1.3.0                crayon_1.5.2               
[109] GetoptLong_1.0.5            rlang_1.1.3                
[111] KEGGREST_1.42.0