Linkage disequilibrium & Haplotypes

[Dave Curtis]

dmachugh at mail.tcd.ie (David MacHugh) wrote:

>We have haplotypic data from a number of microsatellites typed in human
>males on the X-chromosome. 
>Basically we would like to determine the extent of linkage disequilibrium
>among these markers (STRs) using the GENEPOP program.

>Does anyone know of any theoretical objections to recoding the data as
>pseudo-homozygotes and testing for LD?

This sounds to me like it must tbe wrong - you're treating each
observation as if it were two observations.

>Perhaps someone might know a more appropriate method for dealing with this
>type of data.

I could think about it. Are you talking about examining each pair of
loci separately, or a group together?


Dave Curtis
http://www.gene.ucl.ac.uk/~dcurtis