rsnps (version 0.0.5)

NCBI_snp_query: Query NCBI's dbSNP for information on a set of SNPs

Description

This function queries NCBI's dbSNP 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

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.
  • Marker:The name of the marker. If the rs ID queried has been merged, the up-to-date name of the marker is returned here, and a warning is issued.
  • Class:The marker's 'class'. Seehttp://www.ncbi.nlm.nih.gov/projects/SNP/snp_legend.cgi?legend=snpClassfor more details.
  • Gene:If the marker 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 marker 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.
  • Major:The major allele of the SNP, on the forward strand, given it is an SNV; otherwise,NA.
  • Minor:The minor allele of the SNP, on the forward strand, 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.
  • BP:The chromosomal position, in base pairs, of the marker, as aligned with the current genome used by dbSNP.

See Also

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

Examples

## 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'