Question: Calculating association with outcome variable and Phased Haplotypes
1
gravatar for viavialin
4.7 years ago by
viavialin70
Canada
viavialin70 wrote:

I am trying to determine association between a set of haplotypes (2 or 3 marker SNPs) with a clinical outcome. I have phased the haplotypes using Phase v2.1.1 and calculated OR, p values using a 2x2 Fisher's exact test. 

My supervisor says that I should be considering the reference haplotype (major allele frequency) and fixing the OR=1. I managed to do this using several software such as R (haplo.stats) and Unphased, which provide an option to set the reference haplotype. 

However, I do not think that these software phase the haplotypes at all. Is it common to do both - phased haplotypes and set a reference group? I have seen several articles with methods that describe one or the other but not both at the same time. What is the convention and what software would be suitable?

Best,

Sylvia

 

phasing haplotypes • 1.4k views
ADD COMMENTlink written 4.7 years ago by viavialin70
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 790 users visited in the last hour