Ginv                    Compute Generalized Inverse of Input Matrix 
allele.recode           Recode allele values to integer ranks 
dglm.fit                Density function for GLM fit 
geno.count.pairs        Counts of Total Haplotype Pairs Produced by
                        Genotypes 
geno.recode             Recode Genotypes 
glm.fit.nowarn          Modified from glm.fit function to not warn
                        users for binomial non-integer weights. 
haplo.em                EM Computation of Haplotype Probabilities, with
                        Progressive Insertion of Loci 
haplo.em.control        Create the Control Parameters for the EM
                        Computation of Haplotype Probabilities, with
                        Progressive Insertion of Loci 
haplo.em.fitter         Compute engine for haplotype EM algorithm 
haplo.enum              Enumerate all possible pairs of haplotypes that
                        are consistent with a set of un-phased
                        multilocus markers 
haplo.glm               GLM Regression of Trait on Ambiguous Haplotypes 
haplo.glm.control       Create list of control parameters for haplo.glm 
haplo.group             Frequencies for Haplotypes by Grouping Variable 
haplo.hash              Integer Rank Codes for Haplotypes 
haplo.model.frame       Sets up a model frame for haplo.glm 
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       Score Statistics for Association of Traits with
                        Haplotypes 
hla.demo                HLA Loci and Serologic Response to Measles
                        Vaccination. 
locator.haplo           Find Location from Mouse Clicks and Print
                        Haplotypes on Plot 
loci                    Create a group of locus objects from a genotype
                        matrix, assign to 'model.matrix' class. 
locus                   Creates an object of class "locus" 
louis.info              Louis Information for haplo.glm 
mf.gindx                Model Frame Genotype Index to Account for
                        Missing Data in haplo.glm 
na.geno.keep            Find non-missing rows in the genotype matrix of
                        the model.frame 
plot.haplo.score        Plot Haplotype Frequencies versus Haplotype
                        Score Statistics 
plot.haplo.score.slide
                        Plot a haplo.score.slide Object 
print.haplo.em          Print contents of a haplo.em object 
print.haplo.glm         Print a contents of 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 the contents of a haplo.score.slide
                        object 
printBanner             Print a nice banner 
residScaledGlmFit       Scaled Residuals for GLM fit 
score.sim.control       Create the list of control parameters for
                        simulations in haplo.score 
setupData               Set up an example dataset provided within the
                        library. 
setupGeno               Create a group of locus objects from a genotype
                        matrix, assign to 'model.matrix' class. 
summary.haplo.em        Summarize contents of a haplo.em object 
summaryGeno             Summarize Full Haplotype Enumeration on
                        Genotype Matrix 
varfunc.glm.fit         Variance Function for GLM 
