Entering edit mode
7.5 years ago
apilarmoreno4
•
0
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.
Do you have a file relating SNPs to genes?
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.