Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: How to analysis SNP data
0
gravatar for myrezabehboodi
7 months 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 • 178 views
ADD COMMENT • link •
modified 7 months ago by Kevin Blighe ♦ 70k • written 7 months ago by myrezabehboodi • 10
1
gravatar for Kevin Blighe
7 months ago by
Kevin Blighe ♦ 70k
Republic of Ireland
Kevin Blighe ♦ 70k 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 7 months ago • written 7 months ago by Kevin Blighe ♦ 70k
1

Thank you so much dear Kevin.

ADD REPLY • link written 7 months ago by myrezabehboodi • 10
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1076 users visited in the last hour
_