Forum: What is the better association analysis to use for SNPs using gPLINK?
1
gravatar for kc
4.1 years ago by
kc20
United States
kc20 wrote:

I am  trying to work  on SNPs case-control studies. I am working on benign and malignant Melanoma samples and our goal is to differentiate benign and malignant by looking at SNPs. I just want to get SNPs list that are unique in malignant but not benign.I am using gPLINK but I am not sure whether I am using the correct analysis for my SNPs data. The samples are unrelated to each other. I will show the steps what I figured out so far is the way to do in gPLINK for my analysis.

  1. make bed files 
  2. Quality control steps: MAF, GENO, MIND and HWE
  3. Again make bed file after filtering
  4. Association tests: Allelic association tests or logistic regression(not sure which one to use)
  5. look into p-values, OR ratio and/ chisquare values​
  6. Manhattan plot- for significant snps
  7. LD plot( also not sure about this)

 

Questions:

  1. What kind of association test I should do if I want to just look at phenotypic effects or just genotypic effects or both??
  2. Since those samples are unrelated to each other, I think I don't have to do stratification test right??
  3. In which case it is good to look at LD plot?

 

Really appreciate your help!!

snp plink forum • 1.7k views
ADD COMMENTlink modified 4.1 years ago by RamRS21k • written 4.1 years ago by kc20
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