File: TODO

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TO DO:
======

(In no particular order)

- provide HTML linkage disequilibrium table

- consider enhancing LD tables with HWE on diagonal, potentially use
  lower trangular are to colorie on a second veriabe, e.g. p-value on
  top, D' on the bottom.

- create LD.haplotype function.

- chromosome, chromosome.map

- Transmission/Disequilibrium Test

- interface to genehunter

- Haplotype estimation via EM and Gibbs/MCMC

- Gene-map displays:  given a list of genes, and their location on the chromosome, plot the markers along the chromosome.
  You know, something like

	   m1   m2      m4          m6
	---|----|-|------|-|--------|
	          m3       m5

- Quantitative and categorical gene-map plots.  The above with a plot above it, something like


	Disequlibrium:
			                   |
			   |             | o
			   o    | |      o |
			   |    o o      |          |
			        | |                 o
			                            |
			   m1   m2      m4          m6
			---|----|-|------|-|--------|
		          m3       m5

* import/export scripts to the linkage .par and .pre files

* easy grouping of genotypes, like


DONE
====

  DONE - update documentation for HWE.test

  DONE  - re-write HWE test to be more general. (It currently supports only
two alleles)

  DONE - Additional HWE test algorithms(permutation, exact)	

  Accomplished by making HWE test a wrapper for chisq.test.

  DONE - compute/test pairwise disequlibrium

  DONE - Disequilibrium estimation & testing