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.cc                Haplotype Association Analysis in a
                        Case-Control design
haplo.chistat           Calculate a score test statistic for
                        haplotypes
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.scan              Search for a trait-locus by sliding a
                        fixed-width window over each marker locus and
                        scanning all possible haplotype lengths within
                        the window
haplo.scan.obs          For observed data, slide a fixed-width window
                        over each marker locus and scan all possible
                        haplotypes within the window
haplo.scan.sim          For simulated data, slide a fixed-width window
                        over each marker locus and scan all possible
                        haplotypes within the window
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            Remove rows with NA in covariates, but keep
                        genotypes with NAs
plot.haplo.score        Plot Haplotype Frequencies versus Haplotype
                        Score Statistics
plot.haplo.score.slide
                        Plot a haplo.score.slide Object
print.haplo.cc          Print a haplo.cc 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.scan        Print a haplo.scan 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
