BAFfromClusterMeans     B Allele Frequency & Log R Ratio Calculation
BAFfromGenotypes        B Allele Frequency & Log R Ratio Calculation
GWASTools-defunct       Defunct Functions in Package 'GWASTools'
GWASTools-package       Tools for Genome Wide Association Studies
GdsGenotypeReader       Class GdsGenotypeReader
GdsIntensityReader      Class GdsIntensityReader
GdsReader               Class GdsReader
GenotypeData-class      Class GenotypeData
GenotypeIterator-class
                        Class GenotypeIterator
HLA                     HLA region base positions
IntensityData-class     Class IntensityData
MatrixGenotypeReader    Class MatrixGenotypeReader
NcdfGenotypeReader      Class NcdfGenotypeReader
NcdfIntensityReader     Class NcdfIntensityReader
NcdfReader              Class NcdfReader
ScanAnnotationDataFrame
                        Class ScanAnotationDataFrame
ScanAnnotationSQLite    Class ScanAnotationSQLite
SnpAnnotationDataFrame
                        Class SnpAnotationDataFrame
SnpAnnotationSQLite     Class SnpAnotationSQLite
alleleFrequency         Allelic frequency
allequal                Test if two objects have the same elements
anomDetectBAF           BAF Method for Chromosome Anomaly Detection
anomDetectLOH           LOH Method for Chromosome Anomaly Detection
anomIdentifyLowQuality
                        Identify low quality samples
anomSegStats            Calculate LRR and BAF statistics for anomalous
                        segments
apartSnpSelection       Random selection of SNPs
asSnpMatrix             Utilities for snpStats
assocCoxPH              Cox proportional hazards
assocRegression         Association testing with regression
batchChisqTest          Batch Effects of Genotyping
centromeres             Centromere base positions
chromIntensityPlot      Plot B Allele Frequency and/or Log R Ratio, R
                        or Theta values for samples by probe position
                        on a chromosome
convertNcdfGds          Convert between NetCDF and GDS format
createDataFile          Write genotypic calls and/or associated metrics
                        to a GDS or netCDF file.
duplicateDiscordance    Duplicate discordance
duplicateDiscordanceAcrossDatasets
                        Functions to check discordance and allelic
                        dosage correlation across datasets
duplicateDiscordanceProbability
                        Probability of duplicate discordance
exactHWE                Hardy-Weinberg Equilibrium testing
findBAFvariance         Find chromosomal areas with high BAlleleFreq
                        (or LogRRatio) standard deviation
gdsSubset               Write a subset of data in a GDS file to a new
                        GDS file
genoClusterPlot         SNP cluster plots
genotypeToCharacter     Convert number of A alleles to character
                        genotypes
getVariable             Accessors for variables in GenotypeData and
                        IntensityData classes and their component
                        classes
getobj                  Get an R object stored in an Rdata file
hetByScanChrom          Heterozygosity rates by scan and chromosome
hetBySnpSex             Heterozygosity by SNP and sex
ibdPlot                 Plot theoretical and observed identity by
                        descent values and assign relationships
imputedDosageFile       Create and check a GDS or NetCDF file with
                        imputed dosages
intensityOutliersPlot   Plot mean intensity and highlight outliers
manhattanPlot           Manhattan plot for genome wide association
                        tests
meanIntensityByScanChrom
                        Calculate Means & Standard Deviations of
                        Intensities
mendelErr               Mendelian Error Checking
mendelList              Mendelian Error Checking
missingGenotypeByScanChrom
                        Missing Counts per Scan per Chromosome
missingGenotypeBySnpSex
                        Missing Counts per SNP by Sex
pasteSorted             Paste two vectors sorted pairwise
pcaSnpFilters           Regions of SNP-PC correlation to filter for
                        Principal Component Analysis
pedigreeCheck           Testing for internal consistency of pedigrees
pedigreeDeleteDuplicates
                        Remove duplicates from a pedigree
pedigreeMaxUnrelated    Find a maximal set of unrelated individuals in
                        a subset of a pedigree.
pedigreePairwiseRelatedness
                        Assign relatedness from pedigree data
plinkWrite              Utilities to create and check PLINK files
pseudoautoIntensityPlot
                        Plot B Allele Frequency and Log R Ratio for the
                        X and Y chromosomes, overlaying XY SNPs
pseudoautosomal         Pseudoautosomal region base positions
qqPlot                  QQ plot for genome wide assocation studies
qualityScoreByScan      Mean and median quality score for scans
qualityScoreBySnp       Mean and median quality score for SNPs
readWriteFirst          Read and write the first n lines of a file
relationsMeanVar        Mean and Variance information for full-sibs,
                        half-sibs, first-cousins
saveas                  Save an R object with a new name
setMissingGenotypes     Write a new netCDF or GDS file, setting certain
                        SNPs to missing
simulateGenotypeMatrix
                        Simulate Genotype or Intensity Matrix & Load
                        into GDS/NetCDF File
snpCorrelationPlot      SNP correlation plot
vcfWrite                Utility to write VCF file
