I have a series of SNP's that I have investigated. One of them is the COMT, of which a particular haplotype is commonly quoted in the literature.
I had collected blood samples for DNA analysis in 200 patients, all of which unrelated. I used TaqMan for a rtPCR analysis, so now I have 200 patients in which I have genotyped for these SNPs.
I am hoping to analysis them per haplotype, to check my outcomes: I am used to R, but I am not sure how to do this properly.
Am I correct in saying that I cannot calculate the actual haplotype for each patient, but rather estimate group frequencies, and then check for association with outcome between groups?
Any help?
It seems like you don't know the gametic phase of the SNPs. Are the SNPs you genotyped linked?
No I do not know the gametic phase. By linked, do you mean in linkage equilirbium? Some are strongly in LD, but others are less so.
By linked, I meant are they from the same gene or nearby on the same chromosome. If you don't know the gametic phase, then you can't obtain haplotypes unless, perhaps you use an external resource to probabilistically infer the haplotypes.
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