Hi everyone,

I am analyzing methylation data obtained by using enrichment based methods using QSEA package. While performing annotation, I am getting the following error.

result=makeTable(QSEAset, glm=qseaGLM,
+                  groupMeans=getSampleGroups(QSEAset), keep=sig,
+                  annotation=hg38_anno_final,
+                  norm_method="beta")

Run:
adding test results from TvN
obtaining raw values for 3 samples in 1353 windows
deriving beta values...
adding annotation
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': sequences chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22 have incompatible genomes:
  - in 'x': BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38
  - in 'y': BSgenome.Hsapiens.UCSC.NA, BSgenome.Hsapiens.UCSC.NA, BSgen

For qsea object creation, I have used 'BSgenome.Hsapiens.UCSC.hg38', and got the annotation file (hg38_anno_final) using 'TxDb.Hsapiens.UCSC.hg38.knownGene'. I also have changed all the seqinfo in the hg38_anno_final file using following

seqinfo(hg38_anno_final$hg38_genes_5UTRs)@genome<-paste0("BSgenome.Hsapiens.UCSC.",seqinfo(hg38_anno_final$hg38_genes_5UTRs)@genome)

I am unable to figure out the origin of problem. Any help will be highly appreciated.

sessionInfo( )

R version 4.0.5 (2021-03-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
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 
[8] methods   base     

other attached packages:
 [1] shiny_1.6.0                             
 [2] AnnotationHub_2.22.1                    
 [3] BiocFileCache_1.14.0                    
 [4] dbplyr_2.1.1                            
 [5] BSgenome.Hsapiens.UCSC.hg19_1.4.3       
 [6] org.Hs.eg.db_3.12.0                     
 [7] TxDb.Hsapiens.UCSC.hg38.knownGene_3.10.0
 [8] GenomicFeatures_1.42.3                  
 [9] AnnotationDbi_1.52.0                    
[10] Biobase_2.50.0                          
[11] annotatr_1.16.0                         
[12] BSgenome.Hsapiens.UCSC.hg38_1.4.3       
[13] BSgenome_1.58.0                         
[14] rtracklayer_1.50.0                      
[15] Biostrings_2.58.0                       
[16] XVector_0.30.0                          
[17] GenomicRanges_1.42.0                    
[18] GenomeInfoDb_1.26.7                     
[19] IRanges_2.24.1                          
[20] S4Vectors_0.28.1                        
[21] BiocGenerics_0.36.1                     
[22] qsea_1.16.0                             

loaded via a namespace (and not attached):
 [1] bitops_1.0-7                           
 [2] matrixStats_0.59.0                     
 [3] bit64_4.0.5                            
 [4] progress_1.2.2                         
 [5] httr_1.4.2                             
 [6] bslib_0.2.5.1                          
 [7] tools_4.0.5                            
 [8] DT_0.18                                
 [9] utf8_1.2.1                             
[10] R6_2.5.0                               
[11] colorspace_2.0-1                       
[12] DBI_1.1.1                              
[13] withr_2.4.2                            
[14] tidyselect_1.1.1                       
[15] prettyunits_1.1.1                      
[16] bit_4.0.4                              
[17] curl_4.3.1                             
[18] compiler_4.0.5                         
[19] cli_2.5.0                              
[20] xml2_1.3.2                             
[21] DelayedArray_0.16.3                    
[22] sass_0.4.0                             
[23] scales_1.1.1                           
[24] readr_1.4.0                            
[25] askpass_1.1                            
[26] rappdirs_0.3.3                         
[27] stringr_1.4.0                          
[28] digest_0.6.27                          
[29] Rsamtools_2.6.0                        
[30] pkgconfig_2.0.3                        
[31] htmltools_0.5.1.1                      
[32] MatrixGenerics_1.2.1                   
[33] regioneR_1.22.0                        
[34] fastmap_1.1.0                          
[35] limma_3.46.0                           
[36] htmlwidgets_1.5.3                      
[37] rlang_0.4.11                           
[38] rstudioapi_0.13                        
[39] RSQLite_2.2.7                          
[40] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[41] jquerylib_0.1.4                        
[42] generics_0.1.0                         
[43] jsonlite_1.7.2                         
[44] zoo_1.8-9                              
[45] crosstalk_1.1.1                        
[46] BiocParallel_1.24.1                    
[47] gtools_3.9.2                           
[48] dplyr_1.0.6                            
[49] RCurl_1.98-1.3                         
[50] magrittr_2.0.1                         
[51] GenomeInfoDbData_1.2.4                 
[52] Matrix_1.3-4                           
[53] Rcpp_1.0.6                             
[54] munsell_0.5.0                          
[55] fansi_0.5.0                            
[56] lifecycle_1.0.0                        
[57] stringi_1.6.2                          
[58] yaml_2.2.1                             
[59] SummarizedExperiment_1.20.0            
[60] zlibbioc_1.36.0                        
[61] plyr_1.8.6                             
[62] HMMcopy_1.32.0                         
[63] grid_4.0.5                             
[64] blob_1.2.1                             
[65] promises_1.2.0.1                       
[66] crayon_1.4.1                           
[67] lattice_0.20-44                        
[68] hms_1.1.0                              
[69] knitr_1.33                             
[70] pillar_1.6.1                           
[71] reshape2_1.4.4                         
[72] biomaRt_2.46.3                         
[73] XML_3.99-0.6                           
[74] glue_1.4.2                             
[75] BiocVersion_3.12.0                     
[76] data.table_1.14.0                      
[77] BiocManager_1.30.16                    
[78] vctrs_0.3.8                            
[79] httpuv_1.6.1                           
[80] gtable_0.3.0                           
[81] openssl_1.4.4                          
[82] purrr_0.3.4                            
[83] assertthat_0.2.1                       
[84] cachem_1.0.5                           
[85] ggplot2_3.3.4                          
[86] xfun_0.24                              
[87] mime_0.10                              
[88] xtable_1.8-4                           
[89] later_1.2.0                            
[90] tibble_3.1.2                           
[91] GenomicAlignments_1.26.0               
[92] memoise_2.0.0                          
[93] ellipsis_0.3.2                         
[94] interactiveDisplayBase_1.28.0

Thanks

Rakesh

This sort of thing:

seqinfo(hg38_anno_final$hg38_genes_5UTRs)@genome<-paste0("BSgenome.Hsapiens.UCSC.",seqinfo(hg38_anno_final$hg38_genes_5UTRs)@genome)

is something that you should almost never (like 99% of the time) need to do, nor should you do it. In other words, mucking about in an S4 object instead of using the provided accessors is a suboptimal thing to do, unless you are a super l33t expert. Because what you ended up doing was borking all of the seqinfo for your hg38_anno_final object. Which is what the error says:

- in 'y': BSgenome.Hsapiens.UCSC.NA, BSgenome.Hsapiens.UCSC.NA, BSgen

You should probably show why you are trying to change the seqinfo slot like that, and perhaps people can then tell you the right way to do it.