Please help with haplotypes!!!

susy

New Member
#1
Hi guys,

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

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
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