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Mapping snps to genes R packages

Hello,

I am trying to prepare my data in order to perform some GWAS analysis. I have bed/fam/bim files and another file in the following format:

Pathway1 gene1 gene2 ...genei

Pathway2 gene1 gene2...genej . . .

Pathway186 gene1 gene2 ...genek

I want to map snps to their genes using the files that I mentioned above in order to create a new file in this form:

Pathway1 snps ....

Pathway2 snps... . . .

Pathway186 snps...

Is there an R package that will allow me to do this mapping using the files that I have? I would appreciate it if you could recommend me a way for doing this mapping. I have read a lot of forums but I still haven't found a way to do this. Thanks in advance.

snp r gene
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written by apilarmoreno4 • apilarmoreno4

Do you have a file relating SNPs to genes?

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written by ddiez ddiez

Unfortunately no. I was thinking if it was possible to somehow use the bed/bim/fam files to get which snps fall under which gene. For example, the bim file contains information about snp's physical position. Is there a tool that I can use, that is, based on physical position to know/ predict under which gene snps fall? If I can do this, then I can do the mapping later since my ultimate goal is to know identify the snps in a pathway.

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written by apilarmoreno4 • apilarmoreno4

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