Hi I have a dataset with chromosome and position.

VARIANT_ID   chromosome position
17_26797415_147499  17  26797415
17_26797556_147500  17  26797556    

How can I assign rs id using R? This data have more than 500 SNPs.

  • Update: BioMart was used as suggested by @RamRS
  • 'NA NOT FOUND' was a resulting error.
  • @RamRS recommended inputing na.omit in the input vector
  • This appear to have resolved the situation
  • 1
    $\begingroup$ You may want to explore reutils or biomaRt. See this thread on biostars: biostars.org/p/323319 $\endgroup$
    – Ram RS
    Aug 21, 2020 at 19:05
  • $\begingroup$ Thank you. I tried, but I got a strange error message . Query ERROR: caught BioMart::Exception::Usage: Filter NA NOT FOUND $\endgroup$ Aug 21, 2020 at 20:38
  • 2
    $\begingroup$ That's not strange - one your inputs is NA. Wrap the input vector with na.omit and you should not see the error. $\endgroup$
    – Ram RS
    Aug 21, 2020 at 22:48
  • 1
    $\begingroup$ Thank you! I understand it. $\endgroup$ Aug 22, 2020 at 0:26


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