Bonferroni.sig          Bonferroni correction of p values
GenomicControl          Population substructure
Ginv                    Compute Generalized Inverse of Input Matrix
HapMap                  SNPs from HapMap project
HapMap.SNPs.pos         SNPs from HapMap project
LD                      max-statistic for a 2x3 table
SNPs                    SNPs in a case-control study
SNPs.info.pos           SNPs in a case-control study
Table.N.Per             Descriptive sample size and percentage
Table.mean.se           Descriptive sample size, mean, and standard
                        error
WGassociation           Whole genome association analysis
association             Association analysis between a single SNP and a
                        given phenotype
asthma                  SNP data on asthma case-control study
getGeneSymbol           Get gene symbol from a list of SNPs
getNiceTable            Get Latex output
getSignificantSNPs      Extract significant SNPs from an object of
                        class 'WGassociation'
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.glm               GLM Regression of Trait on Ambiguous Haplotypes
haplo.glm.control       Create list of control parameters for haplo.glm
haplo.interaction       Haplotype interaction with a covariate
haplo.model.frame       Sets up a model frame for haplo.glm
haplo.score             Score Statistics for Association of Traits with
                        Haplotypes
haplo.score.slide       Score Statistics for Association of Traits with
                        Haplotypes
hla.demo                HLA Loci and Serologic Response to Measles
                        Vaccination
inheritance             Collapsing (or recoding) genotypes into
                        different categories (generally two) depending
                        on a given genetic mode of inheritance
int                     Identify interaction term
interactionPval         Two-dimensional SNP analysis for association
                        studies
intervals               Print ORs and 95% confidence intervals for an
                        object of class 'haplo.glm'
louis.info              Louis Information for haplo.glm
make.geno               Create a group of locus objects from some SNPs,
                        assign to 'model.matrix' class.
maxstat                 max-statistic for a 2x3 table
na.geno.keep            Remove rows with NA in covariates, but keep
                        genotypes with NAs
odds                    Extract odds ratios, 95% CI and pvalues
permTest                Permutation test analysis
plot.WGassociation      Function to plot -log p values from an object
                        of class 'WGassociation'
plot.haplo.score        Plot Haplotype Frequencies versus Haplotype
                        Score Statistics
plotMissing             Plot of missing genotypes
printBanner             Print a nice banner
qqpval                  Functions for inspecting population
                        substructure
related                 Get related samples
resHapMap               SNPs from HapMap project
scanWGassociation       Whole genome association analysis
score.sim.control       Create the list of control parameters for
                        simulations in haplo.score
setupGeno               Create a group of locus objects from a genotype
                        matrix, assign to 'model.matrix' class.
setupSNP                Convert columns in a dataframe to class 'snp'
snp                     SNP object
sortSNPs                Sort a vector of SNPs by genomic position
tableHWE                Test for Hardy-Weinberg Equilibrium
