Entering edit mode
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