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Thread: Please help with haplotypes!!!

  1. #1
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    Red face Please help with haplotypes!!!




    Hi guys,

    I posted this question yesterday but sadly had no reply
    I really need help here

    I am using HAPSTAT to run a haplotype X environment interaction analysis on a case-control sample. It is a very easy calculation and the software is easy to use, user friendly.

    BUT

    When the calculation is done, in the OUTPUT file, the program codes haplotypes with a series of 0 and 1 (1001, 0011, 1100, 0101...).
    My haplotype is made of 4 SNPS, so it seems logic that those numbers, somehow, represent the 4 alleles.... but which is which?

    Among all the haplotypes possible, there is 1 that I want to consider more than the others, it is the risk haplotype. But how do I recognise it among those strings of numbers???

    Please, any help would be greatly appreciated!

    THANK YOU!!!

  2. #2
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    Re: Please help with haplotypes!!!


    I suggest do not use numbers to avoid confusion: For example, create a text file seperated with tab.
    SNP1-A SNP1-B SNP2-A SNP2-B .......SO ON..
    A G C T...........
    G G C C..........
    A A T T

    and than give as input, haplo.cc(disease_vector, above_file.txt, simulate = TRUE)

    I hope I explained you well.

    Satish

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