BiomaRt - improved access to Ensembl ?
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Entering edit mode
Abiologist • 0
@2b534cfa
Last seen 16 hours ago
Poland

At support.bioconductor.org/p/130050/#9157234 James W. MacDonald gave a function which, if modified, might be of use with useMart ? (the post was referred to as old so I'm asking a new question). Any chance of getting a similar function for useMart rather than useEnsembl ? - or won't this work ? (I get an error saying no Port - details below). Many thanks. I've tried:

library("biomaRt")
getMart <- function(biomart, dataset, host, path, archive) {
e <- simpleError("")
while(is(e, "simpleError")) {
    e <- tryCatch(useMart(biomart, dataset, host, path, archive), error = function(x) x)
}
e}

## Europe:
gene.db <- getMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "https://www.ensembl.org", path = "/biomart/martservice", archive = FALSE); gene.db 
## East USA:
gene.db <- getMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", host = "https://useast.ensembl.org", path = "/biomart/martservice", archive = FALSE); gene.db

## results from East USA:
error httr2_failure
Error in req_perform():
Failed to perform HTTP request.
Caused by error in curl::curl_fetch_memory():
URL rejected: Port number was not a decimal number between 0 and 65535
---
Backtrace:

  1. global getMart(...)
  2.   base::tryCatch(...)
  3.   base (local) tryCatchList(expr, classes, parentenv, handlers)
  4.   base (local) tryCatchOne(expr, names, parentenv, handlers[[1 L]])
  5.   base (local) doTryCatch(return(expr), name, parentenv, handler)
  6.   biomaRt::useMart(biomart, dataset, host, path, archive)
  7.     biomaRt:::.useMart(...)
  8.       biomaRt:::.listMarts(...)
  9.         biomaRt:::bmRequest(...)
 10.           httr2::req_perform(request)
 11.             base::tryCatch(...)
 12.               base (local) tryCatchList(expr, classes, parentenv, handlers)
 13.                 base (local) tryCatchOne(expr, names, parentenv, handlers[[1 L]])
 14.                   value[[3 L]](cond)

sessionInfo( )
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Sonoma 14.6.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Europe/Berlin
tzcode source: internal

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

other attached packages:
[1] biomaRt_2.60.1

loaded via a namespace (and not attached):
 [1] bit_4.5.0               jsonlite_1.8.9         
 [3] dplyr_1.1.4             compiler_4.4.1         
 [5] crayon_1.5.3            filelock_1.0.3         
 [7] tidyselect_1.2.1        Biobase_2.64.0         
 [9] xml2_1.3.6              blob_1.2.4             
[11] stringr_1.5.1           Biostrings_2.72.1      
[13] IRanges_2.38.1          progress_1.2.3         
[15] png_0.1-8               fastmap_1.2.0          
[17] R6_2.5.1                XVector_0.44.0         
[19] generics_0.1.3          curl_5.2.3             
[21] httr2_1.0.4             GenomeInfoDb_1.40.1    
[23] BiocGenerics_0.50.0     tibble_3.2.1           
[25] AnnotationDbi_1.66.0    GenomeInfoDbData_1.2.12
[27] DBI_1.2.3               pillar_1.9.0           
[29] rlang_1.1.4             utf8_1.2.4             
[31] KEGGREST_1.44.1         cachem_1.1.0           
[33] stringi_1.8.4           bit64_4.5.2            
[35] RSQLite_2.3.7           memoise_2.0.1          
[37] cli_3.6.3               magrittr_2.0.3         
[39] zlibbioc_1.50.0         digest_0.6.37          
[41] dbplyr_2.5.0            rappdirs_0.3.3         
[43] hms_1.1.3               BiocFileCache_2.12.0   
[45] lifecycle_1.0.4         S4Vectors_0.42.1       
[47] prettyunits_1.2.0       vctrs_0.6.5            
[49] glue_1.7.0              stats4_4.4.1           
[51] fansi_1.0.6             httr_1.4.7             
[53] tools_4.4.1             pkgconfig_2.0.3        
[55] UCSC.utils_1.0.0
biomaRt • 140 views
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Entering edit mode

Why do you want to use useMart() rather than useEnsembl()? They are essentially the same (useEnsembl() will eventually call useMart()), but with some Ensembl specific defaults. The intention is for useEnsembl() to be more straightforward to connect to the most common BioMart instance. Is that not the case for you?

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