What is the difference between the haplotype constructions of usual Case -control method and the tool FBAT (Family -Based Association Tool)?
Standard case-control association studies just look at one group versus the other - they don't take family information into account. FBAT is an association test that does take family information into account and will analyse the family structure to check which alleles are transmitted in the disease phenotype (or not). FBAT also allows you to adjust for covariates and to include interaction terms in the modelling, again within the context of the family structures.
The last time that I checked, FBAT and PBAT have not been updated in the recent past. The developer seemed to have returned to Europe (from Harvard). An alternative approach is to generate pseudocontrols from your data and then run a conditional logistic regression analysis, i.e., in place of FBAT. This is what I did for a recent association study in the same university where FBAT was developed. Take a look at my code here: https://github.com/kevinblighe/GwasTriosCLogit
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Another assignment? What have you tried?
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what does WHYT mean?
Oh I see - based on the user's posting history it seems that he/she is looking to answer questions in a test. We need to be more explicit about these since other people may not understand the context.
what have you tried? sorry
I am using FBAT tool kit for family based analysis.I want to understand the way this tool constructs haplotype.Could someone help me?