Develop function that has chr:pos as input and rsid as output

[sinarueeger]

The function ncbi_snp_query(snp) takes SNPs as input and outputs chromosome, position and other annotation for each SNP.

Idea: reverse inputs. Have chromosome and position as input and output SNP identifier and other annotation: ncbi_snp_query(chr, pos).

See also #119

Todo

1. develop new function ncbi_snp_query_chrpos
2. let ncbi_snp_query_snp = ncbi_snp_query
3. Rewrite within ncbi_snp_query: call ncbi_snp_query_chrpos if chr+pos are provided and ncbi_snp_query_snp if snps are provided.

[complexgenome]

Hi,

I have never worked with API/call/get/URL before.
This feature is really important, and I would like to help in this.

paste0("https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/", snps_num[i])

I have not idea how to get URL/API to retrieve SNP information based on CHR:POS. I reached out to the NCBI helpdesk they suggested to use entrez:

EDirect Install on Mac, Unix, Linux: https://www.youtube.com/watch?v=rPDXGsLcTQ0
EDirect Install on Windows: https://www.youtube.com/watch?v=hTzqsb1eD10

The best resource I got is https://api.ncbi.nlm.nih.gov/variation/v0/

Any inputs would be helpful.