wed, block time #4

EXERCISE/SELF-LEARNING 2

Use the EHP.R "R subroutine" (here is a local copy, and here is the online manual ) to estimate the haplotype frequency from some data
tmp <- c( rep( c(0,2), 14), rep( c(1,1), 4), rep( c(1,2), 34), rep( c(2,0), 10), rep( c(2,1), 50), rep( c(2,2), 109))
geno <- matrix(tmp, ncol=2, byrow=T)
eh(geno, K=1)
Check the deviation of 1cm=1Mb rule in different human chromosomes: does the deviation increase with shorter chromosome lengths?
Construct another example of the Simpson's paradox
The transmitted and untransmitted allele for an affected offspring presumbly have different allele frequency is that marker is linked to the disease. On the other hand, the transmitted and untranmitted allele for an unaffected offspring are expected to be from the same population with the same allele frequency. Check whether any work has been done to confirm this?
If the minor allele frequency in two subpopulations are 0.3 and 0.4, respectively, what's the F_st value when these two subpopulations are combined into one?
Find any paper that measure the amount of subpopulation (using, e.g. F_st) in Mexican population (using any genetic or bio markers).