I would like to run a WormBaseParasite Biomart in R https://parasite.wormbase.org/biomart/martview/d0d9a510b4b2a07b52f24615ad26107f I got an xml and tried to run in R but errors keep coming up
> library(biomaRt)
> listMarts(host = "parasite.wormbase.org")
Error in `[.data.frame`(marts, , c("biomart", "version")) :
undefined columns selected
> wormbase <- useMart(biomart = "parasite_mart",
+ host = "https://parasite.wormbase.org",
+ port = 443)
Error in .useMart(biomart, dataset, host = host, path = path, port = port, :
Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
And I realise such error appear in the Biocoductor manual too "Using a BioMart other than Ensembl" https://www.bioconductor.org/packages/devel/bioc/vignettes/biomaRt/inst/doc/accessing_other_marts.html Could someone pls help as the website of wormbaseparasite biomart is never working when I try to export the result.
This worked for me:
> library(biomaRt)
> listMarts(host = "parasite.wormbase.org")
biomart version
1 parasite_mart WBPS 19 Mart
> useMart(biomart = "parasite_mart", host = "parasite.wormbase.org")
> sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8 LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.56.1
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 utf8_1.2.4 generics_0.1.3 bitops_1.0-7 xml2_1.3.5 RSQLite_2.3.7 stringi_1.7.12
[8] hms_1.1.3 digest_0.6.33 magrittr_2.0.3 fastmap_1.1.1 blob_1.2.4 progress_1.2.2 AnnotationDbi_1.62.2
[15] GenomeInfoDb_1.36.2 DBI_1.2.1 BiocManager_1.30.22 httr_1.4.7 purrr_1.0.2 fansi_1.0.6 XML_3.99-0.14
[22] Biostrings_2.68.1 cli_3.6.1 rlang_1.1.1 crayon_1.5.2 dbplyr_2.5.0 XVector_0.40.0 Biobase_2.60.0
[29] bit64_4.0.5 cachem_1.0.8 tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 GenomeInfoDbData_1.2.10 filelock_1.0.3
[36] BiocGenerics_0.46.0 curl_5.2.0 vctrs_0.6.5 R6_2.5.1 png_0.1-8 stats4_4.3.0 lifecycle_1.0.4
[43] BiocFileCache_2.8.0 zlibbioc_1.46.0 KEGGREST_1.40.1 stringr_1.5.0 S4Vectors_0.38.1 IRanges_2.34.1 bit_4.0.5
[50] pkgconfig_2.0.3 pillar_1.9.0 glue_1.7.0 tibble_3.2.1 tidyselect_1.2.1 compiler_4.3.0 prettyunits_1.1.1
[57] RCurl_1.98-1.12
my R is most updated version 4.4.0 and I'm using windows PC too, not sure why it doesn't work for me.
>listMarts(host = "parasite.wormbase.org")
Error in `[.data.frame`(marts, , c("biomart", "version")) :
undefined columns selected
even I tried
>listMarts(host = "parasite.wormbase.org")
biomart version
1 parasite_mart WBPS 19 Mart
it shows the same error.
Thanks for reporting this. There was an issue in more recent versions of biomaRt where it failed to parse the list of available datasets advertised by the WormBase ParaSite Mart.
This has now been updated in biomaRt v2.60.1 and should update on Bioconductor in a few days. The vignette will then also update to reflect the fixes.
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