I have some dbSNP ids and I'm trying to locate the reference and the alternate allele . I used the SNPlocs.Hsapiens.dbSNP144.GRCh37 package. But it gave me a message to try the snpcount package.

I've looked at the snpcount package, but unable to find an appropriate example for what I'm looking for. Can anyone help please.

Alternatively, I also have the chromosome number and position. And would like to find the reference and alternate allele for those positions. Can anyone suggest a solution ?

Example code below:

snps <- SNPlocs.Hsapiens.dbSNP144.GRCh37
my_rsids <- c("rs2639606", "rs75264089")
my_snps <- snpsById(snps, my_rsids, ifnotfound="drop")
my_snpsDF <- as.data.frame(my_snps)

alleleInfo <- rsid2alleles(my_rsids, caching=TRUE)

#Error: SNPlocs.Hsapiens.dbSNP144.GRCh37::rsid2alleles() is defunct.
#Please use the SNPlocs API instead. See '?snpcount' for more
#information.

The error message points you to a help page, which should be helpful. Here's a bit more information.

> library(SNPlocs.Hsapiens.dbSNP144.GRCh37)
> library(BSgenome.Hsapiens.UCSC.hg19)
> my_rsids <- c("rs2639606", "rs75264089")
> gpos <- snpsById(SNPlocs.Hsapiens.dbSNP144.GRCh37, my_rsids)

## have to convert to UCSC style chromosomes
> seqlevelsStyle(gpos) <- "UCSC"
> z <- inferRefAndAltAlleles(gpos, BSgenome.Hsapiens.UCSC.hg19)
> mcols(gpos) <- cbind(mcols(gpos), z)
> gpos
UnstitchedGPos object with 2 positions and 5 metadata columns:
      seqnames       pos strand |   RefSNP_id alleles_as_ambig genome_compat
         <Rle> <integer>  <Rle> | <character>      <character>     <logical>
  [1]     chr9  71028127      * |   rs2639606                R          TRUE
  [2]     chr6  25056788      * |  rs75264089                S          TRUE
       ref_allele     alt_alleles
      <character> <CharacterList>
  [1]           A               G
  [2]           C               G
  -------
  seqinfo: 25 sequences (1 circular) from hg19 genome