Ginv                    Compute Generalized Inverse of Input Matrix 
allele.recode           Recode allele values to integer ranks 
dglm.fit		Given a glm Model Fit, Compute the Probability
			Density P(y|Xb)
geno.recode             Recode Genotypes 
geno.count.pairs        Counts of Total Haplotype Pairs 
glm.fit.nowarn		Version of glm.fit for haplo.glm in R with binomial trait
haplo.em                EM Computation of Haplotype Probabilities
haplo.em.control        Control Parameters for haplo.em
haplo.em.fitter		Manage C Routine for Haplotype Frequency Estimation
haplo.enum              Enumerate all haplotype pairs consistent with 
			a set of un-phased multilocus markers
haplo.glm		Perform glm regression of a trait on haplotype effects
haplo.glm.control	Control parameters for haplo.glm
haplo.group		Haplotype Frequencies by Grouping Variable
haplo.hash              Integer Rank Codes for Haplotypes 
haplo.model.frame	Set up a glm model.frame for Ambiguous Haplotypes
haplo.score             Score Statistics for Association of Traits with
                        Haplotypes 
haplo.score.glm         Compute haplotype score statistics for GLM 
haplo.score.merge	Merge haplo.score and haplo.group Objects 
haplo.score.podds       Compute Haplotype Score Statistics for Ordinal
                        Traits with Proportional Odds Model 
haplo.score.slide       Sliding Window of haplo.score Applied to Sub-haplotypes 
hla.demo                HLA Loci and Serologic Response to
                        Measles Vaccination.
locator.haplo           Find Location from Mouse Clicks and Print
                        Haplotypes on Plot 
loci			Pairs of Columns are the Marker Alleles for
			loci in a model.matrix
locus			A Pair of Columns as a Single Locus, as a model.matrix
louis.info		Compute Louis' Information Matrix for glm
			Regression Coefficients
mf.gindx		Get the Genotype Matrix from a model.frame
na.geno.keep.q		Keep Rows of Genotype Matrix if Missing Alleles, but Without Missing
			Values for Response or Other Covaraites
plot.haplo.score        Plot Haplotype Frequencies Versus Haplotype
                        Score Statistics 
plot.haplo.score.slide  Plot -log10(p-value) of haplo.score for Sub-haplotypes
printBanner             Print a Nice Banner
print.haplo.em          Print Haplotype Frequency EM Results
print.haplo.glm         Print a haplo.glm Object
print.haplo.group	Print a haplo.group Object
print.haplo.score       Print a haplo.score Object 
print.haplo.score.merge Print a haplo.score.merge Object
print.haplo.score.slide Print a haplo.score.slide Object
residScaledGlmFit	Given a glm Model Fit, Compute Scaled Residual
score.sim.control       Control Parameters for haplo.score Simulations
setupData		Load a data set into the working directory.
			Does same as data() in R.
setupGeno		Prepare a genotype matrix to be used in
			haplo.glm.  Handles class, and allele type issues.
summaryGeno		Summarize Full Haplotype Enumeration on Genotype Matrix 
summary.haplo.em        Print Extended Results from Haplotype
			Frequency EM Computation
varfunc.glm.fit		Given a glm Model Fit, Compute the Variance
			Function, b''(theta),  Where theta = X'B
