The following code (which is not from Bioconductor) produces 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, with the addition of data for all alleles of a SNP) plus a table of minor allele frequencies from each source (which would also be nice - but not necessary). Does there exist coding in Bioconductor which could extract the data from NCBI for all the alleles of a SNP ? Many thanks.

remotes::install_github("ropensci/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

Hi, the GenomicScores package provides supporting infrastructure to create annotation resources storing MAF data. You may consult the current available ones in the subsection entitled "Retrieval of minor allele frequency data" from its vignette, which also includes an example using MAF values from gnomAD 4.0. If you have a specific request for a MAF source of data that is not currently available in Bioconductor, please open an issue in the GitHub repo of GenomicScores.

robert.

I've discovered that rsnps::ncbi_snp_query(snp_id) does actually give this information - at the bottom of the result$maf_population table. I presume there is not an equivalent in Bioconductor (?)