Error creating Seurat Object for Signac

[ahmadsam66]

Hello @satijalab,

I have used the standard pipeline at https://satijalab.org/signac/articles/pbmc_vignette.html. When I run :

pbmc <- CreateSeuratObject(
  counts = chrom_assay,
  assay = "peaks",  meta.data = metadata 
)

I faced with following error :

Some cells in meta.data not present in provided counts matrix.Error in `[[<-`(`*tmp*`, "orig.ident", value = idents) : 
  [[<- defined for objects of type "S4" only for subclasses of environment

How can I fix this problem?

R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] patchwork_1.1.1            ggplot2_3.3.3              EnsDb.Mmusculus.v75_2.99.0
 [4] ensembldb_2.14.0           AnnotationFilter_1.14.0    GenomicFeatures_1.42.1    
 [7] AnnotationDbi_1.52.0       Biobase_2.50.0             GenomicRanges_1.42.0      
[10] GenomeInfoDb_1.26.2        IRanges_2.24.1             S4Vectors_0.28.1          
[13] BiocGenerics_0.36.0        Seurat_3.2.3               Signac_1.1.1              

loaded via a namespace (and not attached):
  [1] reticulate_1.18             tidyselect_1.1.0            RSQLite_2.2.3              
  [4] htmlwidgets_1.5.3           grid_4.0.3                  BiocParallel_1.24.1        
  [7] Rtsne_0.15                  munsell_0.5.0               codetools_0.2-18           
 [10] ica_1.0-2                   future_1.21.0               miniUI_0.1.1.1             
 [13] withr_2.4.1                 colorspace_2.0-0            OrganismDbi_1.32.0         
 [16] knitr_1.31                  rstudioapi_0.13             ROCR_1.0-11                
 [19] tensor_1.5                  listenv_0.8.0               MatrixGenerics_1.2.1       
 [22] GenomeInfoDbData_1.2.4      polyclip_1.10-0             farver_2.0.3               
 [25] bit64_4.0.5                 parallelly_1.23.0           vctrs_0.3.6                
 [28] generics_0.1.0              xfun_0.21                   biovizBase_1.38.0          
 [31] BiocFileCache_1.14.0        lsa_0.73.2                  ggseqlogo_0.1              
 [34] R6_2.5.0                    rsvd_1.0.3                  hdf5r_1.3.2                
 [37] reshape_0.8.8               bitops_1.0-6                spatstat.utils_2.0-0       
 [40] cachem_1.0.3                DelayedArray_0.16.1         assertthat_0.2.1           
 [43] promises_1.1.1              scales_1.1.1                nnet_7.3-15                
 [46] gtable_0.3.0                globals_0.14.0              goftest_1.2-2              
 [49] ggbio_1.38.0                rlang_0.4.10                RcppRoll_0.3.0             
 [52] splines_4.0.3               rtracklayer_1.50.0          lazyeval_0.2.2             
 [55] dichromat_2.0-0             checkmate_2.0.0             BiocManager_1.30.10        
 [58] yaml_2.2.1                  reshape2_1.4.4              abind_1.4-5                
 [61] backports_1.2.1             httpuv_1.5.5                Hmisc_4.4-2                
 [64] RBGL_1.66.0                 tools_4.0.3                 ellipsis_0.3.1             
 [67] RColorBrewer_1.1-2          ggridges_0.5.3              Rcpp_1.0.6                 
 [70] plyr_1.8.6                  base64enc_0.1-3             progress_1.2.2             
 [73] zlibbioc_1.36.0             purrr_0.3.4                 RCurl_1.98-1.2             
 [76] prettyunits_1.1.1           rpart_4.1-15                openssl_1.4.3              
 [79] deldir_0.2-9                pbapply_1.4-3               cowplot_1.1.1              
 [82] zoo_1.8-8                   SeuratObject_4.0.0          SummarizedExperiment_1.20.0
 [85] ggrepel_0.9.1               cluster_2.1.0               tinytex_0.29               
 [88] magrittr_2.0.1              data.table_1.13.6           scattermore_0.7            
 [91] lmtest_0.9-38               RANN_2.6.1                  SnowballC_0.7.0            
 [94] ProtGenerics_1.22.0         fitdistrplus_1.1-3          matrixStats_0.58.0         
 [97] hms_1.0.0                   mime_0.10                   evaluate_0.14              
[100] xtable_1.8-4                XML_3.99-0.5                jpeg_0.1-8.1               
[103] gridExtra_2.3               compiler_4.0.3              biomaRt_2.46.3             
[106] tibble_3.0.6                KernSmooth_2.23-18          crayon_1.4.1               
[109] htmltools_0.5.1.1           mgcv_1.8-33                 later_1.1.0.1              
[112] Formula_1.2-4               tidyr_1.1.2                 DBI_1.1.1                  
[115] tweenr_1.0.1                dbplyr_2.1.0                MASS_7.3-53                
[118] rappdirs_0.3.3              Matrix_1.3-2                igraph_1.2.6               
[121] pkgconfig_2.0.3             GenomicAlignments_1.26.0    foreign_0.8-81             
[124] plotly_4.9.3                xml2_1.3.2                  XVector_0.30.0             
[127] stringr_1.4.0               VariantAnnotation_1.36.0    digest_0.6.27              
[130] sctransform_0.3.2           RcppAnnoy_0.0.18            graph_1.68.0               
[133] spatstat.data_1.7-0         Biostrings_2.58.0           rmarkdown_2.6              
[136] leiden_0.3.7                fastmatch_1.1-0             htmlTable_2.1.0            
[139] uwot_0.1.10                 curl_4.3                    shiny_1.6.0                
[142] Rsamtools_2.6.0             lifecycle_1.0.0             nlme_3.1-151               
[145] jsonlite_1.7.2              viridisLite_0.3.0           askpass_1.1                
[148] BSgenome_1.58.0             pillar_1.4.7                lattice_0.20-41            
[151] GGally_2.1.1                fastmap_1.1.0               httr_1.4.2                 
[154] survival_3.2-7              glue_1.4.2                  spatstat_1.64-1            
[157] png_0.1-7                   bit_4.0.4                   ggforce_0.3.2              
[160] stringi_1.5.3               blob_1.2.1                  latticeExtra_0.6-29        
[163] memoise_2.0.0               dplyr_1.0.4                 irlba_2.3.3                
[166] future.apply_1.7.0         

[timoast]

Can you try re-installing Signac and restarting R?

[timoast]

Did you restart R and clear the environment?

[ahmadsam66]

yes, I did.

[ahmadsam66]

any other suggestion?

I am using Mouse genome mm10.

I have re-install all packages, but still not working.

[timoast]

Can you try installing Seurat v4 and then re-installing Signac?

[ahmadsam66]

It worked !!, thank you so much.