Signac: RegionStats: Not all seqlevels present in supplied genome, trying to load regions beyond the boundaries of non-circular sequence "chr8"

Question

[yau]

First of all, I would like to show my appreciation towards Signac!

I currently ran RegionStats for my single cell atac-seq data, however, I encountered some error.

I am trying to perform this : https://github.com/stuart-lab/signac/blob/HEAD/vignettes/pbmc_multiomic.Rmd

Error and warning are as below:

Purkinje_multiome <- RegionStats(Purkinje_multiome, genome = BSgenome.Mmusculus.UCSC.mm10)
Warning in RegionStats.default(object = regions, genome = genome, verbose = verbose,  :
  Not all seqlevels present in supplied genome
Error in loadFUN(x, seqname, ranges) : 
  trying to load regions beyond the boundaries of non-circular sequence "chr8"

I used EnsDb.Mmusculus.v79 for the annotation and BSgenome.Mmusculus.UCSC.mm10 as input of RegionStats. Because RegionStats cannot input EnsDb file, also, the vignettes illustrate the use of EnsDb as annotation input and BSgenome as input of RegionStats. I am not sure if this is the problem.

Thanks!!!!

[yau]

session info:
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

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

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

other attached packages:
 [1] BSgenome.Mmusculus.UCSC.mm10_1.4.3 ggdark_0.2.1                       lubridate_1.9.3                   
 [4] forcats_1.0.0                      stringr_1.5.1                      dplyr_1.1.4                       
 [7] purrr_1.0.2                        readr_2.1.5                        tidyr_1.3.1                       
[10] tibble_3.2.1                       ggplot2_3.5.1                      tidyverse_2.0.0                   
[13] BSgenome.Mmusculus.UCSC.mm39_1.4.3 BSgenome_1.72.0                    rtracklayer_1.64.0                
[16] BiocIO_1.14.0                      Biostrings_2.72.1                  XVector_0.44.0                    
[19] EnsDb.Mmusculus.v79_2.99.0         ensembldb_2.28.0                   AnnotationFilter_1.28.0           
[22] GenomicFeatures_1.56.0             AnnotationDbi_1.66.0               Biobase_2.64.0                    
[25] GenomicRanges_1.56.0               GenomeInfoDb_1.40.1                IRanges_2.38.0                    
[28] S4Vectors_0.42.0                   BiocGenerics_0.50.0                Seurat_5.1.0                      
[31] Signac_1.13.0                      SeuratObject_5.0.2                 sp_2.1-4                          

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.4.0               later_1.3.2                 bitops_1.0-7               
  [5] polyclip_1.10-6             XML_3.99-0.16.1             fastDummies_1.7.3           lifecycle_1.0.4            
  [9] globals_0.16.3              lattice_0.22-6              MASS_7.3-60.2               magrittr_2.0.3             
 [13] plotly_4.10.4               yaml_2.3.8                  httpuv_1.6.15               sctransform_0.4.1          
 [17] spam_2.10-0                 spatstat.sparse_3.0-3       reticulate_1.37.0           cowplot_1.1.3              
 [21] pbapply_1.7-2               DBI_1.2.3                   RColorBrewer_1.1-3          abind_1.4-5                
 [25] zlibbioc_1.50.0             Rtsne_0.17                  RCurl_1.98-1.14             GenomeInfoDbData_1.2.12    
 [29] ggrepel_0.9.5               irlba_2.3.5.1               listenv_0.9.1               spatstat.utils_3.0-4       
 [33] goftest_1.2-3               RSpectra_0.16-1             spatstat.random_3.2-3       fitdistrplus_1.1-11        
 [37] parallelly_1.37.1           leiden_0.4.3.1              codetools_0.2-20            DelayedArray_0.30.1        
 [41] RcppRoll_0.3.0              tidyselect_1.2.1            UCSC.utils_1.0.0            matrixStats_1.3.0          
 [45] spatstat.explore_3.2-7      GenomicAlignments_1.40.0    jsonlite_1.8.8              progressr_0.14.0           
 [49] ggridges_0.5.6              survival_3.6-4              tools_4.4.0                 ica_1.0-3                  
 [53] Rcpp_1.0.12                 glue_1.7.0                  gridExtra_2.3               SparseArray_1.4.8          
 [57] MatrixGenerics_1.16.0       withr_3.0.0                 fastmap_1.2.0               fansi_1.0.6                
 [61] digest_0.6.35               timechange_0.3.0            R6_2.5.1                    mime_0.12                  
 [65] colorspace_2.1-0            scattermore_1.2             tensor_1.5                  spatstat.data_3.0-4        
 [69] RSQLite_2.3.7               utf8_1.2.4                  generics_0.1.3              data.table_1.15.4          
 [73] httr_1.4.7                  htmlwidgets_1.6.4           S4Arrays_1.4.1              uwot_0.2.2                 
 [77] pkgconfig_2.0.3             gtable_0.3.5                blob_1.2.4                  lmtest_0.9-40              
 [81] htmltools_0.5.8.1           dotCall64_1.1-1             ProtGenerics_1.36.0         scales_1.3.0               
 [85] png_0.1-8                   rstudioapi_0.16.0           tzdb_0.4.0                  reshape2_1.4.4             
 [89] rjson_0.2.21                nlme_3.1-163                curl_5.2.1                  zoo_1.8-12                 
 [93] cachem_1.1.0                KernSmooth_2.23-22          parallel_4.4.0              miniUI_0.1.1.1             
 [97] restfulr_0.0.15             pillar_1.9.0                grid_4.4.0                  vctrs_0.6.5                
[101] RANN_2.6.1                  promises_1.3.0              xtable_1.8-4                cluster_2.1.6              
[105] cli_3.6.2                   compiler_4.4.0              Rsamtools_2.20.0            rlang_1.1.3                
[109] crayon_1.5.2                future.apply_1.11.2         plyr_1.8.9                  stringi_1.8.4              
[113] viridisLite_0.4.2           deldir_2.0-4                BiocParallel_1.38.0         munsell_0.5.1              
[117] lazyeval_0.2.2              spatstat.geom_3.2-9         Matrix_1.7-0                RcppHNSW_0.6.0             
[121] hms_1.1.3                   patchwork_1.2.0             bit64_4.0.5                 future_1.33.2              
[125] KEGGREST_1.44.0             shiny_1.8.1.1               SummarizedExperiment_1.34.0 ROCR_1.0-11                
[129] igraph_2.0.3                memoise_2.0.1               fastmatch_1.1-4             bit_4.0.5   

[yau]

> Purkinje_multiome@assays[["peaks"]]@ranges@seqnames@values
 [1] 1          2          3          4          5          6          7          8          9          10         11        
[12] 12         13         14         15         16         17         18         19         X          Y          MT        
[23] GL456211.1 JH584304.1 GL456212.1
Levels: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Y MT GL456211.1 GL456212.1 JH584304.1

> Purkinje_multiome@assays[["peaks"]]@annotation@seqnames
factor-Rle of length 1763965 with 22 runs
  Lengths:  83099  68561  56688 128222 149106  89406  49376 121281 ...  78167  75582  61589  34433 132985  49365  49256     26
  Values :     3      X      16     7      11     6      13     4  ...     10     8      15     18     1      12     19     MT
Levels(22): 3 X 16 7 11 6 13 4 9 Y 17 5 2 14 10 8 15 18 1 12 19 MT

> BSgenome.Mmusculus.UCSC.mm10
| BSgenome object for Mouse
| - organism: Mus musculus
| - provider: UCSC
| - genome: mm10
| - release date: Sep 2017
| - 239 sequence(s):
|     1                                    2                                    3                                   
|     4                                    5                                    6                                   
|     7                                    8                                    9                                   
|     10                                   11                                   12                                  
|     13                                   14                                   15                                  
|     ...                                  ...                                  ...                                 
|     MG3683_PATCH                         MG3686_PATCH                         MG4209_PATCH                        
|     MG4211_PATCH                         MG4213_PATCH                         MMCHR1_CHORI29_IDD5_1               
|     WSB/EIJ_MMCHR11_CTG1                 WSB/EIJ_MMCHR11_CTG2                 WSB/EIJ_MMCHR11_CTG3                
|     PWK/PHJ_MMCHR11_CTG1                 PWK/PHJ_MMCHR11_CTG2                 PWK/PHJ_MMCHR11_CTG3                
|     CAST/EI_MMCHR11_CTG4                 CAST/EI_MMCHR11_CTG5                                                     
| 
| Tips: call 'seqnames()' on the object to get all the sequence names, call 'seqinfo()' to get the full sequence info, use the '$'
| or '[[' operator to access a given sequence, see '?BSgenome' for more information.