R help - Nov 2024 - R coding to extract allele frequencies from NCBI for ALL alleles of one SNP?

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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If you haven't already done so,  this might be better posted on
Bioconductor:
https://www.bioconductor.org/

Cheers,
Bert

On Fri, Nov 15, 2024 at 2:53?AM Clark Jeremy <jeremy.clark at pum.edu.pl>
wrote:
> 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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>
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