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Question: How to analysis SNP data
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gravatar for myrezabehboodi
5 weeks ago by
myrezabehboodi • 10
myrezabehboodi • 10 wrote:

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
snp • 99 views
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modified 5 weeks ago by Kevin Blighe ♦ 63k • written 5 weeks ago by myrezabehboodi • 10
1
gravatar for Kevin Blighe
5 weeks ago by
Kevin Blighe ♦ 63k
Kevin Blighe ♦ 63k wrote:

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
ADD COMMENT • link modified 5 weeks ago • written 5 weeks ago by Kevin Blighe ♦ 63k
1

Thank you so much dear Kevin.

ADD REPLY • link written 4 weeks ago by myrezabehboodi • 10
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