Question

snpsBySeqname() and snpsByOverlaps() functions in BSgenome package did not work in my computer

1

Entering edit mode

sunyingkai • 0

@af6d9623

Last seen 23 months ago

Hong Kong

I want to get SNPs information with snpsByOverlaps() and snpsBySeqname() function, but it relied as below:

#my code
library(SNPlocs.Hsapiens.dbSNP144.GRCh38)
library(BSgenome.Hsapiens.NCBI.GRCh38)
snps <- SNPlocs.Hsapiens.dbSNP144.GRCh38

snpsBySeqname(snps,c('1','MT'))
#results
#Error in extract_rowids(x_rowids_env, rowidx) : 
#  is.integer(idx) is not TRUE

snpsByOverlaps(snps, "X:3e6-8e6", genome="GRCh38")

#snpsByOverlaps(snps, "X:3e6-8e6", genome="GRCh38")
#Error in extract_rowids(x_rowids_env, rowidx) : 
#  is.integer(idx) is not TRUE

My computer is Mac with m2 silicon and snpsById() function worked without problem.

BSgeome • 1.2k views

ADD COMMENT • link 23 months ago sunyingkai • 0

0

Entering edit mode

I have no error running your code what is your sessionInfo() ?

ADD REPLY • link 23 months ago Basti ▴ 780

0

Entering edit mode

My sessionInfo() is as below:

R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.0

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12 BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000      
 [3] SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20     SNPlocs.Hsapiens.dbSNP155.GRCh38_0.99.23    
 [5] BSgenome_1.66.2                              rtracklayer_1.58.0                          
 [7] Biostrings_2.66.0                            XVector_0.38.0                              
 [9] GenomicRanges_1.50.2                         GenomeInfoDb_1.34.9                         
[11] IRanges_2.32.0                               S4Vectors_0.36.1                            
[13] BiocGenerics_0.44.0                          biomaRt_2.54.0                              
[15] MRutils_0.2.0.0                              reshape2_1.4.4                              
[17] forcats_1.0.0                                stringr_1.5.0                               
[19] dplyr_1.1.0                                  purrr_1.0.1                                 
[21] readr_2.1.4                                  tidyr_1.3.0                                 
[23] tibble_3.1.8                                 ggplot2_3.4.1                               
[25] tidyverse_1.3.2                             

loaded via a namespace (and not attached):
  [1] googledrive_2.0.0           colorspace_2.1-0            rjson_0.2.21                ellipsis_0.3.2             
  [5] futile.logger_1.4.3         fs_1.6.1                    rstudioapi_0.14             bedr_1.0.7                 
  [9] bit64_4.0.5                 AnnotationDbi_1.60.0        fansi_1.0.4                 lubridate_1.9.2            
 [13] xml2_1.3.3                  codetools_0.2-19            R.methodsS3_1.8.2           cachem_1.0.6               
 [17] jsonlite_1.8.4              Rsamtools_2.14.0            broom_1.0.3                 dbplyr_2.3.0               
 [21] settings_0.2.7              png_0.1-8                   R.oo_1.25.0                 BiocManager_1.30.19        
 [25] compiler_4.2.2              httr_1.4.4                  backports_1.4.1             assertthat_0.2.1           
 [29] Matrix_1.5-3                fastmap_1.1.0               gargle_1.3.0                cli_3.6.0                  
 [33] formatR_1.14                prettyunits_1.1.1           tools_4.2.2                 gtable_0.3.1               
 [37] glue_1.6.2                  GenomeInfoDbData_1.2.9      rappdirs_0.3.3              Rcpp_1.0.10                
 [41] Biobase_2.58.0              cellranger_1.1.0            vctrs_0.5.2                 brio_1.1.3                 
 [45] rvest_1.0.3                 testthat_3.1.6              timechange_0.2.0            lifecycle_1.0.3            
 [49] restfulr_0.0.15             XML_3.99-0.13               googlesheets4_1.0.1         zlibbioc_1.44.0            
 [53] scales_1.2.1                VariantAnnotation_1.44.0    hms_1.1.2                   MatrixGenerics_1.10.0      
 [57] parallel_4.2.2              SummarizedExperiment_1.28.0 lambda.r_1.2.4              yaml_2.3.7                 
 [61] curl_5.0.0                  memoise_2.0.1               stringi_1.7.12              RSQLite_2.2.20             
 [65] BiocIO_1.8.0                gwasvcf_0.1.1               GenomicFeatures_1.50.4      filelock_1.0.2             
 [69] BiocParallel_1.32.5         rlang_1.0.6                 pkgconfig_2.0.3             matrixStats_0.63.0         
 [73] bitops_1.0-7                lattice_0.20-45             GenomicAlignments_1.34.0    bit_4.0.5                  
 [77] tidyselect_1.2.0            plyr_1.8.8                  magrittr_2.0.3              R6_2.5.1                   
 [81] generics_0.1.3              DelayedArray_0.24.0         DBI_1.1.3                   withr_2.5.0                
 [85] pillar_1.8.1                haven_2.5.1                 KEGGREST_1.38.0             RCurl_1.98-1.10            
 [89] validate_1.1.1              modelr_0.1.10               crayon_1.5.2                futile.options_1.0.1       
 [93] utf8_1.2.3                  BiocFileCache_2.6.0         tzdb_0.3.0                  progress_1.2.2             
 [97] grid_4.2.2                  readxl_1.4.2                data.table_1.14.6           blob_1.2.3                 
[101] reprex_2.0.2                digest_0.6.31               VennDiagram_1.7.3           R.utils_2.12.2             
[105] munsell_0.5.0

ADD REPLY • link 23 months ago sunyingkai • 0