[R] R coding to extract allele frequencies from NCBI for ALL alleles of one SNP?

[Clark Jeremy]

Dear All,

The following code extracts from NCBI very nice output for ONE allele of a SNP (often the allele with the second largest frequency - usually termed the minor allele). It gives an average minor allele frequency from all NCBI sources (which is what I want, except I'd like the addition of data for all the other alleles of one SNP) plus a table of minor allele frequencies from each source (which would also be nice - but not necessary). Does there exist a package in R with coding which could extract the data from NCBI for all the alleles of one SNP ? I've looked at getBM() from package biomaRt and searched via Google and Copilot- so far with no success. Many thanks.

remotes::install_github("ropensci/rsnps")
library("rsnps")
# Define the SNP ID
snp_id <- "rs11134679" ## this SNP has alleles A, C, G and T, but results are only for A
# Query the dbSNP database
result <- rsnps::ncbi_snp_query(snp_id)
result2 <- as.data.frame(result)
result2
result2$maf_population



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