I was able to use to VariantAnnotation::predictCoding to find the mutations from the nucleotides into the codons and subsequently the amino acids. However, I want to find the frequency at which these specific mutations occur in the general population. How can I do that using R?
I have an output tsv file which contains the location of the mutation, the variant allele, the reference nucleotide and the nucleotide it changed to, the reference and variant codon, and the reference and variant amino acids as well. If it helps, I also have access to the genes names and the gene id as well. I want to be able to find the frequency of the specific mutation in the population as a whole within R and not have to use an outside websites or sorts.
Are there any specific packages and functions that can help find the frequency? Any help is appreciated. This is my first post, so if I am missing any other information that may be helpful, please let me know.