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NicolasP
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@nicolasp-20123
Last seen 5.6 years ago
Hello, I'm running biomaRt as follow, to retrieve rs IDs with providing SNPs chromosome number and position
ensembl = useMart(biomart = "ENSEMBL_MART_SNP", host = "grch37.ensembl.org", path = "/biomart/martservice",dataset = "hsapiens_snp")
getBM(attributes = c("refsnp_id", "chr_name", "chrom_start", "chrom_end", "allele", "allele_1", "minor_allele", "minor_allele_freq", "chrom_strand"),
filters = "chromosomal_region",
values = chrpos_rsidNA,
mart = ensembl)
head(chrpos_rsidNA)
[1] "21:14714623:14714623" "21:14756926:14756926" "21:14760841:14760841"
[4] "21:14802991:14802991" "21:15471360:15471360" "21:15535590:15535590"
I get the following error message
Error in getBM(attributes = c("refsnp_id", "chr_name", "chrom_start", : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS
Matrix products: default
BLAS: /home/R/R-3.5.1/lib/R/lib/libRblas.so
LAPACK: /home/R/R-3.5.1/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bindrcpp_0.2.2 biomaRt_2.38.0 dplyr_0.8.0.1 data.table_1.12.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.0 pillar_1.3.1 compiler_3.5.1
[4] bindr_0.1.1 prettyunits_1.0.2 bitops_1.0-6
[7] tools_3.5.1 progress_1.2.0 digest_0.6.18
[10] bit_1.1-14 RSQLite_2.1.1 memoise_1.1.0
[13] tibble_2.0.1 pkgconfig_2.0.2 rlang_0.3.1
[16] DBI_1.0.0 curl_3.3 parallel_3.5.1
[19] xml2_1.2.0 httr_1.4.0 stringr_1.4.0
[22] S4Vectors_0.20.1 IRanges_2.16.0 hms_0.4.2
[25] stats4_3.5.1 bit64_0.9-7 tidyselect_0.2.5
[28] glue_1.3.0 Biobase_2.42.0 R6_2.4.0
[31] AnnotationDbi_1.44.0 XML_3.98-1.18 purrr_0.3.1
[34] blob_1.1.1 magrittr_1.5 BiocGenerics_0.28.0
[37] assertthat_0.2.0 stringi_1.3.1 RCurl_1.95-4.12
[40] crayon_1.3.4
Thanks
How long is the
chrpos_rsidNA
vector? It's possible you're hitting Ensembl's time limit for your query, although normally you would receive a message saying this. Does it work if you use a subset of the values inchrpos_rsidNA
?As an aside, it's good to tag your question with the name of the package you're trying to use. Then the maintainer of that package gets notified, I only saw this post by chance.