bugNumerical Library for Haploid Genetics - Bugs: bug #34879, ld_sub_geno () should calculate...


bug #34879: ld_sub_geno () should calculate recursively

Submitted by:  Joel J. Adamson <trashbird1240>
Submitted on:  Tue Nov 22 14:57:50 2011  
Category: LibrarySeverity: 3 - Normal
Item Group: NoneStatus: None
Privacy: PublicAssigned to: Joel J. Adamson <trashbird1240>
Open/Closed: Open

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Tue Nov 22 15:18:41 2011, comment #1:

Check to make sure this reduces to Bennett's Equation.

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.
Tue Nov 22 14:57:50 2011, original submission:

ld_sub_geno () does not calculate the full linkage disequilibrium among a set of loci, it calculates a subset of it. We can use the following recursive algorithm to calculate the right value (where U is the set of loci we're interested in, and |U| is its size):

  1. If |U| = 0, or |U| = 1 then return 0
  2. If |U| = 2 then use the standard linkage disequilibrium
  3. If |U| > 2 then split off a locus and use the following formula

E[X_i \Pi_{j \in U/i} (X_j - p_j) ] - p_i D_U/i

with recursion on the last term. U/i is the set difference of U and i, X_i is an indicator variable giving the status to the locus (on or off) and E represents expectation (genotypic average).

For each such calculation we will need the genotypic frequency (for averaging) and the allele frequencies of the constituent alleles (can be calculated once).

Joel J. Adamson <trashbird1240>
Project AdministratorIn charge of this item.


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