Ginv                    Compute Generalized Inverse of Input Matrix
anova.haplo.glm         Analysis of variance for haplo.glm model fit
chisq.power             Power and sample size for the chi-square
                        distribution
dglm.fit                Internal functions for the HaploStats package.
                        See the help file for the main functions
                        (haplo.em, haplo.score, haplo.glm) for details
                        on some of these functions.
f.power                 Power and sample size for the F distribution
find.haplo.beta.qt      Find beta coefficients for risk haplotypes, for
                        specified r2
fitted.haplo.glm        Fitted values from haplo.glm fit
geno.count.pairs        Counts of Total Haplotype Pairs Produced by
                        Genotypes
geno1to2                convert genotype matrix from 1-column 2-column
get.hapPair             Get a list of objects for haplotype pairs
hapPower.demo           Set of haplotypes and frequencies for power and
                        sample size calculations
haplo.cc                Haplotype Association Analysis in a
                        Case-Control design
haplo.design            Build a design matrix 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.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.power.cc          Compute either power or sample size for
                        haplotype associations in a case-control study.
haplo.power.qt          Compute either power or sample size for
                        haplotype associations with a quantitative
                        trait.
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.score             Score Statistics for Association of Traits with
                        Haplotypes
haplo.score.merge       Merge haplo.score And haplo.group Objects
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
locus                   Creates an object of class "locus"
louis.info              Louis Information for 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
plot.seqhap             Plot a seqhap object
print.haplo.cc          Print a haplo.cc object
print.haplo.em          Print contents of a haplo.em 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
residuals.haplo.glm     Accessing residuals for haplo.glm fit
score.sim.control       Create the list of control parameters for
                        simulations in haplo.score
seqhap                  Sequential Haplotype Scan Association Analysis
                        for Case-Control Data
seqhap.dat              Simulated data for seqhap examples
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
summary.haplo.glm       Print and summary of a haplo.glm object
summaryGeno             Summarize Full Haplotype Enumeration on
                        Genotype Matrix
vcov.haplo.glm          variance-covariance matrix of a fitted
                        haplo.glm object
x.sexcheck              consistency checks for x.linked locus
