Bonferroni.sig          Bonferroni correction of p values
GenomicControl          Population substructure
HapMap                  SNPs from HapMap project
LD                      max-statistic for a 2x3 table
SNPs                    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
getSignificantSNPs      Extract significant SNPs from an object of
                        class 'WGassociation'
haplo.interaction       Haplotype interaction with a covariate
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'
make.geno               Create a group of locus objects from some SNPs,
                        assign to 'model.matrix' class.
maxstat                 max-statistic for a 2x3 table
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'
plotMissing             Plot of missing genotypes
qqpval                  Functions for inspecting population
                        substructure
scanWGassociation       Whole genome association analysis
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
