So I was wondering if anyone can help me.
I have a data file containing a list of SNP's in different alleles at a particular locus. Probably more accurate to say a matrix like so...
SNP Allele C/G A/C C/G 1 0 1 1 2 0 0 1 3 0 1 0
Where " 1, 2,3" is the allele name and " 0 ,1" represents wither that SNP is present in that allele.
So I then have a file of different samples containing the haplotypes and need to do some genetic association tests. The haplotypes have either "1" or "2" alleles from the mother of father (I have 20 alleles so another sample could contain haplotype "14" and "3" from the mother and father). I then have a file that contains immune responses from the individual samples and want to test if the presence of an SNP has an affect on the immune response. For example if SNP C/G is present there is a better response.
I'm really confused on how to link all this data. Especially linking the SNP matrix to the haplotypes. If I could get the genotypes I'd be able to look a frequencies etc.
Any ideas anyone?