Good afternoon,
I am contacting you for an information:
Every time I try to get information on a SNP using biomaRt, the R console
crashes. The session info are:
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
And the commands that I use are:
library(biomaRt)
snp.db =
useMart("ENSEMBL_MART_SNP",host="www.ensembl.org",dataset="hsapiens_snp")
variant = list(9,133271654)
var_info =
getBM(c("chr_name","chrom_start","allele","minor_allele","minor_allele_freq"),c("chr_name","chrom_start"),variant,snp.db)
R always crashes at this point, also on other computers. I am using R 3.0.1 and
the biomaRt package is up to date.
I really don't understand if this is a problem of the server or if I am doing
something wrong.
Thanks a lot for the assistance!
Francesco Mazzarotto
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