Question: Obtaining The Snp Rs Number With The Chromosomal Position
4
gravatar for Sheila
6.9 years ago by
Sheila310
United States
Sheila310 wrote:

This question is similar to this one (Get rs number based on position).

I have a text file with SNPs in the chr:position format

 10:71086
 10:72876
 10:75794

I was wondering if there is an R package (or perhaps one in Bioconductor) that can take these as input values and provide the SNP rs number associate with them????

R bioconductor snps • 30k views
ADD COMMENTlink modified 16 months ago by hsiaoyi050450 • written 6.9 years ago by Sheila310
2
gravatar for Ashutosh Pandey
6.9 years ago by
Philadelphia
Ashutosh Pandey12k wrote:

I think JC has already pointed out a nice resource. The other option would be

Get rs number based on position

ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by Ashutosh Pandey12k
3
gravatar for JC
6.9 years ago by
JC9.7k
Mexico
JC9.7k wrote:

It's not in R, but Kaviar (http://db.systemsbiology.net/kaviar/) can give you the RS information using the coordinates and can be accessed locally or remotely.

ADD COMMENTlink written 6.9 years ago by JC9.7k
1
gravatar for hsiaoyi0504
16 months ago by
hsiaoyi050450
Taiwan
hsiaoyi050450 wrote:

I would like to share another approach. Using EDirect (https://dataguide.nlm.nih.gov/edirect/install.html).

Then you can get the result by running following command:

esearch -db snp -query chr_id[CHR] AND organism[ORGN] AND chr_pos[CPOS]

(modify chr_id, organism, chr_pos to fit your application).

For python, take a look of this function I wrote before https://github.com/hsiaoyi0504/bcinfo/blob/546c54c2f72febd361da59e18b9901591837f826/bcinfo/search.py#L5.

ADD COMMENTlink written 16 months ago by hsiaoyi050450
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