Unable to find inherited method for functions 'seqinfo'

[ftakaes1]

Dear Signac team,

Thank you for all your efforts in maintaining this wonderful package. I am attempting a joint RNA and ATAC-seq analysis by strictly following the suggested vignette. However, when I attempt to create a chromatin assay I get the following error:

Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'genome': unable to find an inherited method for function 'seqinfo' for signature 'x = "ChromatinAssay"'

My code is the following:

library(Seurat)
library(Signac)
library(GenomicRanges)
library(EnsDb.Hsapiens.v86)
library(BSgenome.Hsapiens.UCSC.hg38)


floed_counts <- Read10X_h5("D:/Multiomics/cellranger_output/s001_FLOED/outs/filtered_feature_bc_matrix.h5")
fragpath <- "D:/Multiomics/cellranger_output/s001_FLOED/outs/atac_fragments.tsv.gz"

annotation <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)
seqlevels(annotation) <- paste0('chr', seqlevels(annotation))

floed <- CreateSeuratObject(
  counts = floed_counts$`Gene Expression`,
  assay = "RNA"
)

floed[["ATAC"]] <- CreateChromatinAssay(
  counts = floed_counts$Peaks,
  sep = c(":", "-"),
  fragments = fragpath,
  annotation = annotation
)

At first, I thought this was a package conflict with the seqinfo method being called, but even after using the conflicted package's conflicts_prefer() method to call the exact Signac or GenomeInfoDb seqinfo method I still get this error. Do you have any suggestions to fix this? I noticed a previous user also experienced this error but only after creating a Seurat Object.

I have been stuck on this for a while, so thank you for any help you can provide.

sessionInfo()

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg38_1.4.5
 [2] BSgenome_1.76.0                  
 [3] rtracklayer_1.68.0               
 [4] BiocIO_1.18.0                    
 [5] Biostrings_2.76.0                
 [6] XVector_0.48.0                   
 [7] EnsDb.Hsapiens.v86_2.99.0        
 [8] ensembldb_2.32.0                 
 [9] AnnotationFilter_1.32.0          
[10] GenomicFeatures_1.60.0           
[11] AnnotationDbi_1.70.0             
[12] Biobase_2.68.0                   
[13] Signac_1.16.0                    
[14] Seurat_5.4.0                     
[15] SeuratObject_5.3.0               
[16] sp_2.2-0                         
[17] GenomicRanges_1.60.0             
[18] GenomeInfoDb_1.44.1              
[19] IRanges_2.42.0                   
[20] S4Vectors_0.46.0                 
[21] BiocGenerics_0.54.0              
[22] generics_0.1.4                   

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22            splines_4.5.1              
  [3] later_1.4.4                 bitops_1.0-9               
  [5] tibble_3.3.1                polyclip_1.10-7            
  [7] rpart_4.1.24                XML_3.99-0.20              
  [9] fastDummies_1.7.5           lifecycle_1.0.5            
 [11] hdf5r_1.3.12                globals_0.18.0             
 [13] lattice_0.22-7              MASS_7.3-65                
 [15] backports_1.5.0             magrittr_2.0.4             
 [17] rmarkdown_2.29              Hmisc_5.2-5                
 [19] plotly_4.11.0               yaml_2.3.10                
 [21] httpuv_1.6.16               otel_0.2.0                 
 [23] sctransform_0.4.2           spam_2.11-3                
 [25] spatstat.sparse_3.1-0       reticulate_1.44.1          
 [27] cowplot_1.2.0               pbapply_1.7-4              
 [29] DBI_1.2.3                   RColorBrewer_1.1-3         
 [31] abind_1.4-8                 Rtsne_0.17                 
 [33] purrr_1.2.1                 biovizBase_1.56.0          
 [35] RCurl_1.98-1.17             nnet_7.3-20                
 [37] VariantAnnotation_1.54.1    GenomeInfoDbData_1.2.14    
 [39] ggrepel_0.9.6               irlba_2.3.5.1              
 [41] listenv_0.10.0              spatstat.utils_3.2-0       
 [43] goftest_1.2-3               RSpectra_0.16-2            
 [45] spatstat.random_3.4-3       fitdistrplus_1.2-4         
 [47] parallelly_1.46.1           codetools_0.2-20           
 [49] DelayedArray_0.34.1         RcppRoll_0.3.1             
 [51] tidyselect_1.2.1            UCSC.utils_1.4.0           
 [53] farver_2.1.2                base64enc_0.1-3            
 [55] matrixStats_1.5.0           spatstat.explore_3.6-0     
 [57] GenomicAlignments_1.44.0    jsonlite_2.0.0             
 [59] Formula_1.2-5               progressr_0.18.0           
 [61] ggridges_0.5.7              survival_3.8-3             
 [63] tools_4.5.1                 ica_1.0-3                  
 [65] Rcpp_1.1.1                  glue_1.8.0                 
 [67] gridExtra_2.3               SparseArray_1.8.1          
 [69] xfun_0.52                   MatrixGenerics_1.20.0      
 [71] dplyr_1.1.4                 withr_3.0.2                
 [73] fastmap_1.2.0               digest_0.6.37              
 [75] R6_2.6.1                    mime_0.13                  
 [77] colorspace_2.1-2            scattermore_1.2            
 [79] tensor_1.5.1                dichromat_2.0-0.1          
 [81] spatstat.data_3.1-9         RSQLite_2.4.5              
 [83] tidyr_1.3.2                 data.table_1.18.0          
 [85] httr_1.4.7                  htmlwidgets_1.6.4          
 [87] S4Arrays_1.8.1              uwot_0.2.4                 
 [89] pkgconfig_2.0.3             gtable_0.3.6               
 [91] blob_1.2.4                  lmtest_0.9-40              
 [93] S7_0.2.1                    htmltools_0.5.8.1          
 [95] dotCall64_1.2               ProtGenerics_1.40.0        
 [97] scales_1.4.0                png_0.1-8                  
 [99] spatstat.univar_3.1-5       knitr_1.50                 
[101] rstudioapi_0.17.1           reshape2_1.4.5             
[103] rjson_0.2.23                checkmate_2.3.3            
[105] nlme_3.1-168                curl_6.4.0                 
[107] zoo_1.8-15                  cachem_1.1.0               
[109] stringr_1.6.0               KernSmooth_2.23-26         
[111] parallel_4.5.1              miniUI_0.1.2               
[113] foreign_0.8-90              restfulr_0.0.16            
[115] pillar_1.11.1               grid_4.5.1                 
[117] vctrs_0.6.5                 RANN_2.6.2                 
[119] promises_1.5.0              xtable_1.8-4               
[121] cluster_2.1.8.1             htmlTable_2.4.3            
[123] evaluate_1.0.4              cli_3.6.5                  
[125] compiler_4.5.1              Rsamtools_2.24.0           
[127] rlang_1.1.6                 crayon_1.5.3               
[129] future.apply_1.20.1         plyr_1.8.9                 
[131] stringi_1.8.7               viridisLite_0.4.2          
[133] deldir_2.0-4                BiocParallel_1.42.1        
[135] lazyeval_0.2.2              spatstat.geom_3.6-1        
[137] Matrix_1.7-3                RcppHNSW_0.6.0             
[139] patchwork_1.3.2             bit64_4.6.0-1              
[141] future_1.68.0               ggplot2_4.0.1              
[143] KEGGREST_1.48.1             shiny_1.12.1               
[145] SummarizedExperiment_1.38.1 ROCR_1.0-11                
[147] igraph_2.1.4                memoise_2.0.1              
[149] fastmatch_1.1-6             bit_4.6.0   

[leecon30]

I keep getting this same error code if I try to do anything with my seurat + chromatin assay. If I use seurat merge or seurat subset.

[leecon30]

I fixed it - with the help of ChatGPT.

Run this at the start of each session and it disappears

setMethod(
"seqinfo",
signature(x = "ChromatinAssay"),
function(x) {
GenomeInfoDb::seqinfo(x@ranges)
}
)

[ftakaes1]

Hey Lee,

Thank you for helping to troubleshoot this error. Unfortunately, whenever I use your approach to force a ChromatinAssay to be recognized by seqinfo, I get an error that says:

Error in if (!is.na(x = annotation.genome) & (current.genome != annotation.genome)) { : 
  missing value where TRUE/FALSE needed

It appears that setting a method like that messes up with the annotation or the current genome somehow.

@timoast, whenever you have time, would you kindly give me some pointers on what might be going wrong here?

Thank you for your help!

[ftakaes1]

Quick update: I was able to create the ChromatinAssay by reverting back to version 1.15.0. Still unclear on what went wrong, but I have no seqinfo conflicts in this version.

[leecon30]

Hmmm sorry to hear that. I'm afraid I cannot be of more help.

[ftakaes1]

No worries, thank you for trying to help!

[RoomeRB]

Hi,
I am running essentially the same setup (updated all packages to current) and am getting this error when I make a ChromatinAssay as well. However, in my case it will make the ChromatinAssay and then posts the warning whenever I try to call the ChromatinAssay's name. Moreover, whenever I try to merge two ChromatinAssays it will post the warning.

I have used Leecon30's setMethod code that he recently posted in this comments section and I can once again merge ChromatinAssays without an error.

I appreciate if anyone can share their input on what is causing this error.

[TMWarwick]

We have run into the same error with 1.16.0, only fix was to revert to 1.15.0 and use devtools to install. Attempted the fix kindly suggested by leecon30 but ran into the same TRUE/FALSE error as ftakaes1.

[timoast]

This should be fixed on the develop branch, please install from there and let me know if you still see any errors