Deleted:missing biomart dataset chinese hamster picr
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Charlotte • 0
@68fcf65d
Last seen 3.6 years ago
United Kingdom

Hello,

I'm trying to use the 'cgpicr_gene_ensembl' dataset in biomart and tried exactly as in this post:

Convert mouse gene ids to hamster gene ids

but the dataset is missing ?

> datasets <- listDatasets(useMart('ensembl'))
> datasets[grep('Chinese', datasets[,2]),]
                     dataset                                  description      version
29  cgchok1gshd_gene_ensembl Chinese hamster CHOK1GS genes (CHOK1GS_HDv1) CHOK1GS_HDv1
136   osinensis_gene_ensembl           Chinese medaka genes (ASM858656v1)  ASM858656v1
158   psinensis_gene_ensembl  Chinese softshell turtle genes (PelSin_1.0)   PelSin_1.0

sessionInfo( )
R version 4.1.3 (2022-03-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.50.3 tidyr_1.2.0   

loaded via a namespace (and not attached):
 [1] KEGGREST_1.34.0        progress_1.2.2         tidyselect_1.1.2       purrr_0.3.4            vctrs_0.3.8           
 [6] generics_0.1.2         stats4_4.1.3           BiocFileCache_2.2.1    utf8_1.2.2             blob_1.2.2            
[11] XML_3.99-0.9           rlang_1.0.2            pillar_1.7.0           withr_2.5.0            glue_1.6.2            
[16] DBI_1.1.2              rappdirs_0.3.3         BiocGenerics_0.40.0    bit64_4.0.5            dbplyr_2.1.1          
[21] GenomeInfoDbData_1.2.7 lifecycle_1.0.1        stringr_1.4.0          zlibbioc_1.40.0        Biostrings_2.62.0     
[26] memoise_2.0.1          Biobase_2.54.0         IRanges_2.28.0         fastmap_1.1.0          GenomeInfoDb_1.30.1   
[31] curl_4.3.2             AnnotationDbi_1.56.2   fansi_1.0.3            Rcpp_1.0.8.3           filelock_1.0.2        
[36] BiocManager_1.30.16    cachem_1.0.6           S4Vectors_0.32.3       XVector_0.34.0         bit_4.0.4             
[41] hms_1.1.1              png_0.1-7              digest_0.6.29          stringi_1.7.6          dplyr_1.0.8           
[46] cli_3.2.0              tools_4.1.3            bitops_1.0-7           magrittr_2.0.2         RCurl_1.98-1.6        
[51] tibble_3.1.6           RSQLite_2.2.11         crayon_1.5.0           pkgconfig_2.0.3        ellipsis_0.3.2        
[56] xml2_1.3.3             prettyunits_1.1.1      assertthat_0.2.1       httr_1.4.2             R6_2.5.1              
[61] compiler_4.1.3
biomaRt • 474 views
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