Error in Links(cds) <- links

[qingzengLi]

Firstly thanks for your wonderful packages! I get an error when running Links(cds) <- links:

Error in UseMethod(generic = "Links<-", object = object) : 
  "Links<-"没有适用于"c('cell_data_set', 'SingleCellExperiment', 'RangedSummarizedExperiment', 'SummarizedExperiment', 'RectangularData', 'Vector', 'Annotated', 'vector_OR_Vector')"目标对象的方法

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

other attached packages:
 [1] SeuratObject_4.1.3          Seurat_4.3.0               
 [3] cicero_1.3.9                Gviz_1.42.1                
 [5] monocle3_1.3.1              SingleCellExperiment_1.20.0
 [7] SummarizedExperiment_1.28.0 GenomicRanges_1.50.2       
 [9] GenomeInfoDb_1.34.9         IRanges_2.32.0             
[11] S4Vectors_0.36.2            MatrixGenerics_1.10.0      
[13] matrixStats_0.63.0          Biobase_2.58.0             
[15] BiocGenerics_0.44.0         SeuratWrappers_0.3.1       
[17] Signac_1.9.0               

loaded via a namespace (and not attached):
  [1] utf8_1.2.3               spatstat.explore_3.0-6   reticulate_1.28         
  [4] R.utils_2.12.2           tidyselect_1.2.0         lme4_1.1-31             
  [7] RSQLite_2.3.1            AnnotationDbi_1.60.2     htmlwidgets_1.6.2       
 [10] BiocParallel_1.32.6      Rtsne_0.16               munsell_0.5.0           
 [13] codetools_0.2-19         ica_1.0-3                interp_1.1-4            
 [16] future_1.31.0            miniUI_0.1.1.1           spatstat.random_3.1-3   
 [19] colorspace_2.1-0         progressr_0.13.0         filelock_1.0.2          
 [22] knitr_1.42               rstudioapi_0.14          ROCR_1.0-11             
 [25] tensor_1.5               listenv_0.9.0            GenomeInfoDbData_1.2.9  
 [28] polyclip_1.10-4          bit64_4.0.5              parallelly_1.34.0       
 [31] vctrs_0.6.1              generics_0.1.3           xfun_0.38               
 [34] biovizBase_1.46.0        BiocFileCache_2.6.1      R6_2.5.1                
 [37] rsvd_1.0.5               VGAM_1.1-7               AnnotationFilter_1.22.0 
 [40] bitops_1.0-7             spatstat.utils_3.0-1     cachem_1.0.7            
 [43] DelayedArray_0.24.0      promises_1.2.0.1         BiocIO_1.8.0            
 [46] scales_1.2.1             nnet_7.3-18              gtable_0.3.3            
 [49] globals_0.16.2           goftest_1.2-3            ensembldb_2.22.0        
 [52] rlang_1.1.0              RcppRoll_0.3.0           splines_4.2.0           
 [55] rtracklayer_1.58.0       lazyeval_0.2.2           dichromat_2.0-0.1       
 [58] checkmate_2.1.0          spatstat.geom_3.0-6      BiocManager_1.30.19     
 [61] yaml_2.3.7               reshape2_1.4.4           abind_1.4-5             
 [64] GenomicFeatures_1.50.4   backports_1.4.1          httpuv_1.6.9            
 [67] Hmisc_5.0-1              tools_4.2.0              ggplot2_3.4.2           
 [70] ellipsis_0.3.2           RColorBrewer_1.1-3       ggridges_0.5.4          
 [73] Rcpp_1.0.10              plyr_1.8.8               base64enc_0.1-3         
 [76] progress_1.2.2           zlibbioc_1.44.0          purrr_1.0.1             
 [79] RCurl_1.98-1.12          prettyunits_1.1.1        rpart_4.1.19            
 [82] deldir_1.0-6             pbapply_1.7-0            cowplot_1.1.1           
 [85] zoo_1.8-11               ggrepel_0.9.3            cluster_2.1.4           
 [88] magrittr_2.0.3           data.table_1.14.8        scattermore_0.8         
 [91] lmtest_0.9-40            RANN_2.6.1               ProtGenerics_1.30.0     
 [94] fitdistrplus_1.1-8       evaluate_0.20            hms_1.1.3               
 [97] patchwork_1.1.2          mime_0.12                xtable_1.8-4            
[100] XML_3.99-0.14            jpeg_0.1-10              gridExtra_2.3           
[103] compiler_4.2.0           biomaRt_2.54.1           tibble_3.2.1            
[106] KernSmooth_2.23-20       crayon_1.5.2             minqa_1.2.5             
[109] R.oo_1.25.0              htmltools_0.5.5          later_1.3.0             
[112] Formula_1.2-5            tidyr_1.3.0              DBI_1.1.3               
[115] dbplyr_2.3.1             rappdirs_0.3.3           MASS_7.3-58.3           
[118] boot_1.3-28.1            Matrix_1.5-3             cli_3.6.1               
[121] R.methodsS3_1.8.2        parallel_4.2.0           igraph_1.3.5            
[124] pkgconfig_2.0.3          GenomicAlignments_1.34.1 foreign_0.8-84          
[127] sp_1.6-0                 terra_1.5-21             plotly_4.10.1           
[130] spatstat.sparse_3.0-0    xml2_1.3.3               XVector_0.38.0          
[133] VariantAnnotation_1.44.1 stringr_1.5.0            digest_0.6.31           
[136] sctransform_0.3.5        RcppAnnoy_0.0.20         spatstat.data_3.0-0     
[139] Biostrings_2.66.0        rmarkdown_2.21           leiden_0.4.3            
[142] fastmatch_1.1-3          htmlTable_2.4.1          uwot_0.1.14             
[145] restfulr_0.0.15          curl_5.0.0               shiny_1.7.4             
[148] Rsamtools_2.14.0         rjson_0.2.21             nloptr_2.0.3            
[151] lifecycle_1.0.3          nlme_3.1-162             jsonlite_1.8.4          
[154] viridisLite_0.4.1        BSgenome_1.66.3          fansi_1.0.4             
[157] pillar_1.9.0             lattice_0.20-45          KEGGREST_1.38.0         
[160] fastmap_1.1.1            httr_1.4.5               survival_3.5-0          
[163] glue_1.6.2               remotes_2.4.2            png_0.1-8               
[166] bit_4.0.5                stringi_1.7.12           blob_1.2.4              
[169] latticeExtra_0.6-30      memoise_2.0.1            dplyr_1.1.1             
[172] irlba_2.3.5.1            future.apply_1.10.0

Any suggestions or help would be greatly appreciated!

[timoast]

It looks like you're trying to assign a SingleCellExperiment object as the links information for the Signac object. This is not possible, you need to provide a granges object instead (please see the documentation https://stuartlab.org/signac/reference/links)