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Query NCBI's refSNP for information on a set of SNPs via the API

Source: R/ncbi_snp_api.R
ncbi_snp_query.Rd

This function queries NCBI's refSNP for information related to the latest dbSNP build and latest reference genome for information on the vector of snps submitted.

Usage

ncbi_snp_query(snps)

Arguments

snps

(character) A vector of SNPs (rs numbers).

Value

A dataframe with columns:

  • query: The rs ID that was queried.

  • chromosome: The chromosome that the marker lies on.

  • bp: The chromosomal position, in base pairs, of the marker, as aligned with the current genome used by dbSNP. we add 1 to the base pair position in the BP column in the output data.frame to agree with what the dbSNP website has.

  • rsid: Reference SNP cluster ID. If the rs ID queried has been merged, the up-to-date name of the ID is returned here, and a warning is issued.

  • class: The rsid's 'class'. See https://www.ncbi.nlm.nih.gov/projects/SNP/snp_legend.cgi?legend=snpClass for more details.

  • gene: If the rsid lies within a gene (either within the exon or introns of a gene), the name of that gene is returned here; otherwise, NA. Note that the gene may not be returned if the rsid lies too far upstream or downstream of the particular gene of interest.

  • alleles: The alleles associated with the SNP if it is a SNV; otherwise, if it is an INDEL, microsatellite, or other kind of polymorphism the relevant information will be available here.

  • minor: The allele for which the MAF is computed, given it is an SNV; otherwise, NA.

  • maf: The minor allele frequency of the SNP, given it is an SNV. This is drawn from the current global reference population used by NCBI (GnomAD).

  • ancestral_allele: allele as described in the current assembly

  • variation_allele: difference to the current assembly

  • seqname - Chromosome RefSeq reference.

  • hgvs - full hgvs notation for variant

  • assembly - which assembly was used for the annotations

  • ref_seq - sequence in reference assembly

  • maf_population - dataframe of all minor allele frequencies reported, with columns study, reference allele, alternative allele (minor) and minor allele frequency.

Details

This function currently pulling data for Assembly 38 - in particular note that if you think the BP position is wrong, that you may be hoping for the BP position for a different Assembly.

Note that you are limited in the to a max of one query per second and concurrent queries are not allowed. If users want to set curl options when querying for the SNPs they can do so by using httr::set_config/httr::with_config

References

https://www.ncbi.nlm.nih.gov/projects/SNP/

https://pubmed.ncbi.nlm.nih.gov/31738401/ SPDI model

Examples

if (FALSE) {
## an example with both merged SNPs, non-SNV SNPs, regular SNPs,
## SNPs not found, microsatellite
SNPs <- c("rs332", "rs420358", "rs1837253", "rs1209415715", "rs111068718")
ncbi_snp_query(SNPs)
# ncbi_snp_query("123456") ##invalid: must prefix with 'rs'
ncbi_snp_query("rs420358")
ncbi_snp_query("rs332") # warning that its merged into another, try that
ncbi_snp_query("rs121909001")
ncbi_snp_query("rs1837253")
ncbi_snp_query("rs1209415715")
ncbi_snp_query("rs111068718")
ncbi_snp_query(snps = "rs9970807")

ncbi_snp_query("rs121909001")
ncbi_snp_query("rs121909001", verbose = TRUE)
}