ALZH                    Sample from National Institute of Mental Health
                        (NIMH) Genetics Initiative Alzheimer's Disease
Armitage                Cochran-Armitage test for linear trends in
                        proportions and frequencies
CAMP                    Genotype data from the Childhood Asthma
                        Management Program (CAMP)
HWE                     Test the significances of Hardy-Weinberg
                        Equilibrium (dis)equilibrium) statistics
HWE.chisq               Hardy-Weinberg Equilibrium Significance test
                        for a biallelic locus
HWE.exact               Exact test for Hardy-Weinberg Equilibrium for a
                        biallelic locus
LD                      Pairwise linkage disequilibrium between genetic
                        markers.
LD-class                Class "LD" ~~~
LDband-class            Class "LDband" ~~~
LDdist-class            Wrapper to efficiently store the result from
                        performing LD calculatations over sliding
                        windows containing markers within a distance
PGtables                ~~function to do ... ~~
PerlegenExample         Small example data set from Perlegen
PfizerExample           Small example data set from Pfizer
alleleCount             ~~function to do ... ~~
alleleLevels            ~~function to do ... ~~
alleleSummary           Summary of allele information
alleles                 ~~function to do ... ~~
as.geneSet              Convert an existing object to a geneSet
binsearch               Binary Search
callCodes               ~~function to do ... ~~
ci.balance              Experimental Function to Correct Confidence
                        Intervals At or Near Boundaries of the
                        Parameter Space by 'Sliding' the Interval on
                        the Quantile Scale.
convert                 Efficienctly convert strings of characters into
                        integer codes
decodeCallCodes         Converts integer codes in a callCodes matrix to
                        character string representations of geneSet.
desMarkers              Descriptive statistics for markers
description             ~~function to do ... ~~
diseq                   Estimate or Compute Confidence Interval for the
                        Single-Marker Disequilibrium
errorMetrics            ~~function to do ... ~~
extractAlleles          functions for extracting allele levels, allele
                        pairs, and allele codes
fastGrid                Create a matrix giving all combinations of the
                        elements of x
founderGeneSet          Extract founder info from a geneSet object
geneSet-class           Class "geneSet", a class for genetics data
geneSet2Ped             Translate a geneSet object to a ped matrix
genotypeCoding          Get genotype coding
genotypeLevels          ~~function to do ... ~~
genotypeSummary         print the summary of genotypes sorted by
                        markers
genotypes               ~~function to do ... ~~
gregorius               Probability of Observing All Alleles with a
                        Given Frequency in a Sample of a Specified
                        Size.
haplo.em.w              Wrapper for EM computation of haplotype
                        probabilities, with Progressive Insertion
haplo.scan.w            Wrapper for searching 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.slide.w     Wrapper for haplo.score.slide in haplo.stats
                        package, which is used to identify
                        sub-haplotypes from a group of loci
haplo.score.w           Wrapper for computing score statistics to
                        evaluate the association of a trait with
                        haplotypes, when linkage phase is unknown and
                        diploid marker phenotypes are observed among
                        unrelated subjects
hapmapchr22             Chromosome 22 genotypes from International
                        HapMap project
homozygote              Flag observations with specific allele patterns
html                    Generate summary table files for genotype
                        objects
left                    ~~function to do ... ~~
makeMarkerInfo          makeMarkerInfo creates a dataframe of marker
                        information
makeTransTable          makeTransTable creates a single translation
                        table of the markers
makeTransTableList      makeTransTableList creates a list of
                        translation tables
markerInfo              ~~function to do ... ~~
markerNames             ~~function to do ... ~~
markerSummary           Generate allele, genotype, or LD summary
                        objects
missingCodes            ~~function to do ... ~~
nallele                 ~~function to do ... ~~
nmarker                 ~~function to do ... ~~
notes                   ~~function to do ... ~~
ped2geneSet             translate a ped matrix to a geneSet object
phase                   ~~function to do ... ~~
ploidy                  ~~function to do ... ~~
plot.LD                 Textual and graphical display of linkage
                        disequilibrium (LD) objects
qtlex                   Simulated pedigree with genotypes and one qtl
                        covariate
read.pfizer             ~~function to do ... ~~
read.phe                Read '.phe' phenotype file data
readGenes               Import genetic data from standard file formats
readGenes.ped           Function to read pedigree file format
readGenes.perlegen      Read Perlegen data files.
readGenes.pfizer        Read genetics data files that use Pfizer's data
                        format.
sampleInfo              ~~function to do ... ~~
studyInfo               ~~function to do ... ~~
transTables             ~~function to do ... ~~
xbat                    Simulated pedigree with genotypes and
                        covariates
