Allele frequencies for ALL alleles of one SNP ?
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Abiologist • 0
@2b534cfa
Last seen 2 hours ago
Poland

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
Bioconductor • 80 views
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Entering edit mode
Abiologist • 0
@2b534cfa
Last seen 2 hours ago
Poland

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 (?)

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