abf.Wakefield           Calculate approximate Bayes factor (ABF) using
                        method of Wakefield (2009).
abf.normal              Calculate approximate Bayes factor (ABF) for
                        normal prior.
abf.t                   Calculate approximate Bayes factor (ABF) for t
                        distribution prior.
agtstats                Hypertension association statistics for SNPs
                        near the AGT gene.
align.snpdata.coding    Update genotype coding when there are coded
                        allele designation flips.
allelesAB               Paste together (vectors of) A and B alleles
                        after sorting alphabetically.
bp.scores               Genetic risk scores for blood pressure.
cad.scores              Genetic risk scores for coronary artery disease
                        risk
chi2ncp                 Compute non-centrality parameter of chi squared
                        distribution.
coeff.extract           Coefficient extractor for fitted models.
combine.moments2        Builds a matrix of second moments for a set of
                        individuals, from the matrices of second
                        moments for all constituent subsets of
                        individuals.
contrasting.rainbow     Rainbow of colours permuted to maximise
                        contrast.
est.moments2            Estimate regression coefficients using
                        quadratic approximation to likelihood function.
fitmix                  Fit finite mixture of univariate Gaussian
                        densities to data.
fitmix.plot             Plot empirical density and components and total
                        density for finite mixture of univariate
                        Gaussian densities.
fitmix.r2               For finite mixture of univariate Gaussian
                        densities, computes proportion of variance
                        explained by the mixture labels.
fitmix.simulate         Simulate from finite mixture of univariate
                        Gaussian densities.
gls.approx.logistic     Calculate weights and transformed phenotype so
                        that one iteration of generalised least squares
                        approximates a logistic regression.
grs.filter.Qrs          Filter SNPs for inclusion in genetic risk score
                        using heterogeneity test.
grs.make.scores         Make genetic risk scores from individual-level
                        data.
grs.onesnp.apply        Convenience tool to fit a series of single-SNP
                        models.
grs.plot                Diagnostic plot for genetic risk score
                        calculation from summary statistics.
grs.summary             Genetic risk score calculation from summary
                        statistics.
gtx-package             Genetics ToolboX
gtx.params              Parameter format for multi-SNP analyses
hapmap.read.haplotypes
                        Read hapmap haplotypes.
hapmap.snpdata          Extract individual level snp/haplotype data
                        from HapMap
height.scores           Genetic risk score for height.
lipid.cad.scores        Genetic risk scores for serum lipid levels and
                        coronary artery disease outcome
lipid.scores            Genetic risk scores for serum lipid levels
liver.scores            Genetic risk scores for liver enzyme traits.
lm.moments2             Fit normal linear model using pre-built matrix
                        of second moments.
magic.scores            Genetic risk scores for glucose/insulin traits.
make.moments2           Build matrix of second moments from
                        subject-specific data.
mincover                Compute minimum size of cover of overlapping
                        intervals.
moments2                Class for summary statistic matrix of second
                        moments.
mthfrex                 Simulated example finemapping genotype and
                        phenotype data.
multimatch              Match with multiple matching possible.
multipheno.T2           Multi-phenotype test for association
parse.snps              Parse text representation of a SNP embedded in
                        flanking sequences.
read.snpdata.impute     Read genotype dosages in the format output by
                        IMPUTE.
read.snpdata.mach       Read genotype dosages in the format output by
                        MACH
read.snpdata.minimac    Read genotype dosages in the format output by
                        minimac
read.snpdata.plink      Read genotype dosages in the format output by
                        PLINK.
remap.q2t               Remap coordinates from BLAT query sequence to
                        BLAT target sequence.
sanitise.whitespace     Remove leading and trailing spaces; convert
                        double spaces to single spaces.
snpdata                 Class for SNP genotype and phenotype data.
snphwe                  Exact test of Hardy-Weinberg.
snphweCounts            Exact test of Hardy-Weinberg.
snps.BRCA1              Genotyping array annotation for SNPs near the
                        BRCA1 gene.
stepdown.moments2       Stepwise downward model selection using summary
                        statistic matrix.
stepup.moments2         Stepwise upward model selection using summary
                        statistic matrix.
t2d.scores              Genetic risk scores for type 2 diabetes risk.
t2dex                   Simulated example genotype and longitudinal
                        phenotype data.
