Identification of haplotypes with haplo.em function

I have 6 SNPs of 3 gene regions that are in linkage desequilibrium (highly correlated) and i would like to identify haplotypes to further used them in association study instead of the individual SNP. I found that the function haplo.em from the haplo.stats packages allows to identify the haplotypes and their probability (see haplostats.pdf ( section 3 - page 8). I have some questions regarding the data that we should load in R to use this function and the interpretation of the results :

  1. What format of the data should we load ? Could it be a matrix corresponding in rows to the individuals and a column for each SNP (see the attached file data.png attached) with 0 = major homozygote, 1= heterozygote, 2=minor homozygote ? or should it be as Aa, AA or aa directy ? or something else ?
  2. I dont understand the table of results (section 3.2 "Example Usage") in the Rdocumentation ? how are we suppose to know the combination of alleles corresponding to each haplotype ? Except the last column that is the frequency, i dont get what the other columns give us.
  3. Is there a way to obtain a table with the different haplotypes identified, their frequency and for each one, the corresponding combination of alleles for the SNPs ?

The genetic world is something new to me and dealing with it on R is even harder. I would appreciate any help.

Thank you in advance !
Have a nice day,

This topic was automatically closed 21 days after the last reply. New replies are no longer allowed.

If you have a query related to it or one of the replies, start a new topic and refer back with a link.