How to analysis SNP data

Question

[myrezabehboodi]

Hi folks. I want to analyze the SNP data for the multifactorial disease. The data's format is like the following:

1   100292476   AA
1   101064936   AA

rs577266494 1 103380393 GG

1   104303716   GG
1   104864464   CC
1   106737318   TT
                     **.
                     .
                     .**

I would appreciate it if you could help me to find a pipeline or a tutorial for this reason. thank you

Answer 1

[Kevin Blighe]

Given the data in this format, you could do different types of analyses (in R):

1. encode the genotypes as categorical variables and perform a regression
2. determine the minor allele per SNP and then tabulate these per individual / sample (so, each individual would have 0, 1, or 2 minor alleles per SNP), followed by a regression
3. same as point 2, except that you tally / 'sum up' minor and major alleles for each SNP across cases and controls, and then perform a Chi squared test, as on which I elaborate here: A: SNP dataset and Z Score

Kevin

[myrezabehboodi]

Thank you so much dear Kevin.