SNPlocs.Hsapiens.dbSNP155.GRCh38 0.99.21 missing (e.g.) rs149894845
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Paul Shannon ▴ 470
@paul-shannon-5944
Last seen 15 days ago
United States

45/680 rsids were not found in a search for hg38 locations just now. A single example is provided below to demonstrate the problem.

https://www.ncbi.nlm.nih.gov/snp/rs149894845 returns chr7:54902523 (GRCh38.p13) from the April 9th 2021 build 155, the same as that used in SNPlocs.

I hand-checked a few of the failures. My 3 ad hoc examples were all deletions - possibly a clue? rs1351669490, rs149894845, rs35747839

snpsById(SNPlocs.Hsapiens.dbSNP155.GRCh38, "rs149894845")
Error in rowids2rowidx(user_rowids, ids, x_rowids, ifnotfound) : 
  SNP ids not found: rs149894845

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/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] grid      stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocParallel_1.30.0                      BSgenome.Hsapiens.UCSC.hg38_1.4.4       
 [3] SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.21 BSgenome_1.64.0                         
 [5] rtracklayer_1.56.0                       motifbreakR_2.10.0                      
 [7] trena_1.18.0                             glmnet_4.1-4                            
 [9] Matrix_1.4-1                             RUnit_0.4.32                            
[11] ADvariantExplorer_1.0.22                 EnsDb.Hsapiens.v79_2.99.0               
[13] ensembldb_2.20.1                         AnnotationFilter_1.20.0                 
[15] GenomicFeatures_1.48.0                   AnnotationDbi_1.58.0                    
[17] Biobase_2.56.0                           EndophenotypeExplorer_1.0.37            
[19] R6_2.5.1                                 TrenaProjectAD_1.0.2                    
[21] TrenaProjectHG38_1.2.9                   TrenaMultiScore_1.0.48                  
[23] MotifDb_1.38.0                           Biostrings_2.64.0                       
[25] XVector_0.36.0                           GenomicRanges_1.48.0                    
[27] GenomeInfoDb_1.32.1                      IRanges_2.30.0                          
[29] S4Vectors_0.34.0                         BiocGenerics_0.42.0                     
[31] TrenaProject_1.2.6                      

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.3                           R.methodsS3_1.8.1                       
  [3] tidyr_1.2.0                              ggplot2_3.3.6                           
  [5] bit64_4.0.5                              knitr_1.39                              
  [7] irlba_2.3.5                              DelayedArray_0.22.0                     
  [9] R.utils_2.11.0                           data.table_1.14.2                       
 [11] rpart_4.1.16                             KEGGREST_1.36.0                         
 [13] TFBSTools_1.34.0                         RCurl_1.98-1.6                          
 [15] doParallel_1.0.17                        generics_0.1.2                          
 [17] preprocessCore_1.58.0                    RSQLite_2.2.14                          
 [19] bit_4.0.4                                tzdb_0.3.0                              
 [21] xml2_1.3.3                               httpuv_1.6.5                            
 [23] SummarizedExperiment_1.26.1              assertthat_0.2.1                        
 [25] DirichletMultinomial_1.38.0              viridis_0.6.2                           
 [27] xfun_0.30                                hms_1.1.1                               
 [29] promises_1.2.0.1                         fansi_1.0.3                             
 [31] restfulr_0.0.13                          progress_1.2.2                          
 [33] caTools_1.18.2                           dbplyr_2.1.1                            
 [35] DBI_1.1.2                                htmlwidgets_1.5.4                       
 [37] reshape_0.8.9                            gwascat_2.28.0                          
 [39] purrr_0.3.4                              ellipsis_0.3.2                          
 [41] dplyr_1.0.9                              backports_1.4.1                         
 [43] GenomicScores_2.8.0                      annotate_1.74.0                         
 [45] biomaRt_2.52.0                           MatrixGenerics_1.8.0                    
 [47] vctrs_0.4.1                              cachem_1.0.6                            
 [49] Gviz_1.40.1                              checkmate_2.1.0                         
 [51] annotatr_1.22.0                          GenomicAlignments_1.32.0                
 [53] prettyunits_1.1.1                        cluster_2.1.3                           
 [55] dir.expiry_1.4.0                         lazyeval_0.2.2                          
 [57] seqLogo_1.62.0                           crayon_1.5.1                            
 [59] basilisk.utils_1.8.0                     pkgconfig_2.0.3                         
 [61] ProtGenerics_1.28.0                      nnet_7.3-17                             
 [63] rlang_1.0.2                              lifecycle_1.0.1                         
 [65] SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20 filelock_1.0.2                          
 [67] ghdb_1.0.10                              BiocFileCache_2.4.0                     
 [69] dichromat_2.0-0.1                        AnnotationHub_3.4.0                     
 [71] echotabix_0.99.6                         coloc_5.1.0                             
 [73] randomForest_4.7-1                       matrixStats_0.62.0                      
 [75] RPostgreSQL_0.7-3                        Rhdf5lib_1.18.0                         
 [77] base64enc_0.1-3                          png_0.1-7                               
 [79] viridisLite_0.4.0                        rjson_0.2.21                            
 [81] phastCons100way.UCSC.hg38_3.7.1          bitops_1.0-7                            
 [83] splitstackshape_1.4.8                    R.oo_1.24.0                             
 [85] rhdf5filters_1.8.0                       blob_1.2.3                              
 [87] shape_1.4.6                              mixsqp_0.3-43                           
 [89] lars_1.3                                 stringr_1.4.0                           
 [91] regioneR_1.28.0                          readr_2.1.2                             
 [93] jpeg_0.1-9                               echodata_0.99.10                        
 [95] CNEr_1.32.0                              scales_1.2.0                            
 [97] memoise_2.0.1                            magrittr_2.0.3                          
 [99] plyr_1.8.7                               zlibbioc_1.42.0                         
[101] compiler_4.2.0                           echoconda_0.99.6                        
[103] TxDb.Hsapiens.UCSC.hg38.knownGene_3.15.0 BiocIO_1.6.0                            
[105] RColorBrewer_1.1-3                       catalogueR_0.1.1                        
[107] ade4_1.7-19                              Rsamtools_2.12.0                        
[109] cli_3.3.0                                universalmotif_1.14.0                   
[111] patchwork_1.1.1                          htmlTable_2.4.0                         
[113] Formula_1.2-4                            MASS_7.3-57                             
[115] WGCNA_1.70-3                             tidyselect_1.1.2                        
[117] stringi_1.7.6                            yaml_2.3.5                              
[119] ggrepel_0.9.1                            latticeExtra_0.6-29                     
[121] VariantAnnotation_1.42.0                 tools_4.2.0                             
[123] parallel_4.2.0                           rstudioapi_0.13                         
[125] TFMPvalue_0.0.8                          piggyback_0.1.2                         
[127] foreach_1.5.2                            foreign_0.8-82                          
[129] vbsr_0.0.5                               gridExtra_2.3                           
[131] snpStats_1.46.0                          digest_0.6.29                           
[133] BiocManager_1.30.17                      shiny_1.7.1                             
[135] pracma_2.3.8                             motifmatchr_1.18.0                      
[137] Rcpp_1.0.8.3                             BiocVersion_3.15.2                      
[139] later_1.3.0                              motifStack_1.40.0                       
[141] org.Hs.eg.db_3.15.0                      httr_1.4.3                              
[143] biovizBase_1.44.0                        phastCons7way.UCSC.hg38_3.7.1           
[145] colorspace_2.0-3                         XML_3.99-0.9                            
[147] reticulate_1.24                          splines_4.2.0                           
[149] basilisk_1.8.0                           xgboost_1.6.0.1                         
[151] xtable_1.8-4                             jsonlite_1.8.0                          
[153] poweRlaw_0.70.6                          dynamicTreeCut_1.63-1                   
[155] susieR_0.11.92                           Hmisc_4.6-0                             
[157] pillar_1.7.0                             htmltools_0.5.2                         
[159] mime_0.12                                glue_1.6.2                              
[161] fastmap_1.1.0                            lassopv_0.2.0                           
[163] DT_0.22                                  RMySQL_0.10.23                          
[165] interactiveDisplayBase_1.34.0            codetools_0.2-18                        
[167] utf8_1.2.2                               lattice_0.20-45                         
[169] tibble_3.1.7                             curl_4.3.2                              
[171] gtools_3.9.2                             zip_2.2.0                               
[173] GO.db_3.15.0                             openxlsx_4.2.5                          
[175] survival_3.3-1                           munsell_0.5.0                           
[177] fastcluster_1.2.3                        rhdf5_2.40.0                            
[179] GenomeInfoDbData_1.2.8                   iterators_1.0.14                        
[181] HDF5Array_1.24.0                         impute_1.70.0                           
[183] reshape2_1.4.4                           gtable_0.3.0
SNPlocs.Hsapiens.dbSNP155.GRCh38 • 45 views
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