# Tools for Genome Wide Association Studies

## Documentation for package ‘GWASTools’ version 1.10.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D F G H I M N O P Q R S W X Y

GWASTools-package | Tools for Genome Wide Association Studies

## -- A --

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
anomFilterBAF | BAF Method for Chromosome Anomaly Detection
anomIdentifyLowQuality | Identify low quality samples
anomSegmentBAF | BAF Method for Chromosome Anomaly Detection
anomSegStats | Calculate LRR and BAF statistics for anomalous segments
anomStatsPlot | Calculate LRR and BAF statistics for anomalous segments
apartSnpSelection | Random selection of SNPs
asSnpMatrix | Utilities for snpStats
assocTestCPH | Cox proportional hazards
assocTestFisherExact | Association tests
assocTestRegression | Association tests
autosomeCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes
autosomeCode-method | Class GdsGenotypeReader
autosomeCode-method | Class GenotypeData
autosomeCode-method | Class IntensityData
autosomeCode-method | Class MatrixGenotypeReader
autosomeCode-method | Class NcdfGenotypeReader
autosomeCode-method | Class NcdfIntensityReader
autosomeCode-method | Class SnpAnotationDataFrame
autosomeCode-method | Class SnpAnotationSQLite

## -- B --

BAFfromClusterMeans | B Allele Frequency & Log R Ratio Calculation
BAFfromGenotypes | B Allele Frequency & Log R Ratio Calculation
batchChisqTest | Batch Effects of Genotyping
batchFisherTest | Batch Effects of Genotyping

## -- C --

centromeres | Centromere base positions
centromeres.hg18 | Centromere base positions
centromeres.hg19 | Centromere base positions
checkNcdfGds | Convert between NetCDF and GDS format
chromIntensityPlot | Plot B Allele Frequency and/or Log R Ratio, R or Theta values for samples by probe position on a chromosome
close-method | Class GdsReader
close-method | Class GenotypeData
close-method | Class IntensityData
close-method | Class NcdfReader
close-method | Class ScanAnotationSQLite
close-method | Class SnpAnotationSQLite
convertGdsNcdf | Convert between NetCDF and GDS format
convertNcdfGds | Convert between NetCDF and GDS format
convertVcfGds | Conversion from VCF to GDS

## -- D --

duplicateDiscordance | Duplicate discordance
duplicateDiscordanceAcrossDatasets | Duplicate discordance across datasets
duplicateDiscordanceProbability | Probability of duplicate discordance

## -- F --

findBAFvariance | Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation

## -- G --

gdsCheckImputedDosage | Create and check a GDS file with imputed dosages
GdsGenotypeReader | Class GdsGenotypeReader
GdsGenotypeReader-class | Class GdsGenotypeReader
gdsImputedDosage | Create and check a GDS file with imputed dosages
GdsReader | Class GdsReader
GdsReader-class | Class GdsReader
gdsSetMissingGenotypes | Write a new netCDF or GDS file, setting certain SNPs to missing
gdsSubset | Write a subset of data in a GDS file to a new GDS file
gdsSubsetCheck | Write a subset of data in a GDS file to a new GDS file
genoClusterPlot | SNP cluster plots
genoClusterPlotByBatch | SNP cluster plots
GenotypeData | Class GenotypeData
GenotypeData-class | Class GenotypeData
genotypeToCharacter | Convert number of A alleles to character genotypes
getAlleleA | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getAlleleA-method | Class GdsGenotypeReader
getAlleleA-method | Class GenotypeData
getAlleleA-method | Class SnpAnotationDataFrame
getAlleleA-method | Class SnpAnotationSQLite
getAlleleB | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getAlleleB-method | Class GdsGenotypeReader
getAlleleB-method | Class GenotypeData
getAlleleB-method | Class SnpAnotationDataFrame
getAlleleB-method | Class SnpAnotationSQLite
getAnnotation | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getAnnotation-method | Class ScanAnotationDataFrame
getAnnotation-method | Class ScanAnotationSQLite
getAnnotation-method | Class SnpAnotationDataFrame
getAnnotation-method | Class SnpAnotationSQLite
getAttribute | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getAttribute-method | Class GdsReader
getAttribute-method | Class NcdfReader
getBAlleleFreq | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getBAlleleFreq-method | Class IntensityData
getBAlleleFreq-method | Class NcdfIntensityReader
getChromosome | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getChromosome-method | Class GdsGenotypeReader
getChromosome-method | Class GenotypeData
getChromosome-method | Class IntensityData
getChromosome-method | Class MatrixGenotypeReader
getChromosome-method | Class NcdfGenotypeReader
getChromosome-method | Class NcdfIntensityReader
getChromosome-method | Class SnpAnotationDataFrame
getChromosome-method | Class SnpAnotationSQLite
getDimension | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getDimension-method | Class GdsReader
getDimension-method | Class NcdfReader
getDimensionNames | Class NcdfReader
getDimensionNames-method | Class NcdfReader
getGenotype | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getGenotype-method | Class GdsGenotypeReader
getGenotype-method | Class GenotypeData
getGenotype-method | Class MatrixGenotypeReader
getGenotype-method | Class NcdfGenotypeReader
getLogRRatio | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getLogRRatio-method | Class IntensityData
getLogRRatio-method | Class NcdfIntensityReader
getMetadata | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getMetadata-method | Class ScanAnotationDataFrame
getMetadata-method | Class ScanAnotationSQLite
getMetadata-method | Class SnpAnotationDataFrame
getMetadata-method | Class SnpAnotationSQLite
getobj | Get an R object stored in an Rdata file
getPosition | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getPosition-method | Class GdsGenotypeReader
getPosition-method | Class GenotypeData
getPosition-method | Class IntensityData
getPosition-method | Class MatrixGenotypeReader
getPosition-method | Class NcdfGenotypeReader
getPosition-method | Class NcdfIntensityReader
getPosition-method | Class SnpAnotationDataFrame
getPosition-method | Class SnpAnotationSQLite
getQuality | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getQuality-method | Class IntensityData
getQuality-method | Class NcdfIntensityReader
getQuery | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getQuery-method | Class ScanAnotationSQLite
getQuery-method | Class SnpAnotationSQLite
getScanID | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getScanID-method | Class GdsGenotypeReader
getScanID-method | Class GenotypeData
getScanID-method | Class IntensityData
getScanID-method | Class MatrixGenotypeReader
getScanID-method | Class NcdfGenotypeReader
getScanID-method | Class NcdfIntensityReader
getScanID-method | Class ScanAnotationDataFrame
getScanID-method | Class ScanAnotationSQLite
getScanVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getScanVariable-method | Class GenotypeData
getScanVariable-method | Class IntensityData
getScanVariableNames | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getScanVariableNames-method | Class GenotypeData
getScanVariableNames-method | Class IntensityData
getSex | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getSex-method | Class GenotypeData
getSex-method | Class IntensityData
getSex-method | Class ScanAnotationDataFrame
getSex-method | Class ScanAnotationSQLite
getSnpID | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getSnpID-method | Class GdsGenotypeReader
getSnpID-method | Class GenotypeData
getSnpID-method | Class IntensityData
getSnpID-method | Class MatrixGenotypeReader
getSnpID-method | Class NcdfGenotypeReader
getSnpID-method | Class NcdfIntensityReader
getSnpID-method | Class SnpAnotationDataFrame
getSnpID-method | Class SnpAnotationSQLite
getSnpVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getSnpVariable-method | Class GenotypeData
getSnpVariable-method | Class IntensityData
getSnpVariableNames | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getSnpVariableNames-method | Class GenotypeData
getSnpVariableNames-method | Class IntensityData
getVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getVariable-method | Class GdsGenotypeReader
getVariable-method | Class GdsReader
getVariable-method | Class GenotypeData
getVariable-method | Class IntensityData
getVariable-method | Class NcdfGenotypeReader
getVariable-method | Class NcdfIntensityReader
getVariable-method | Class NcdfReader
getVariable-method | Class ScanAnotationDataFrame
getVariable-method | Class ScanAnotationSQLite
getVariable-method | Class SnpAnotationDataFrame
getVariable-method | Class SnpAnotationSQLite
getVariableNames | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getVariableNames-method | Class GdsReader
getVariableNames-method | Class NcdfReader
getVariableNames-method | Class ScanAnotationDataFrame
getVariableNames-method | Class ScanAnotationSQLite
getVariableNames-method | Class SnpAnotationDataFrame
getVariableNames-method | Class SnpAnotationSQLite
getX | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getX-method | Class IntensityData
getX-method | Class NcdfIntensityReader
getY | Accessors for variables in GenotypeData and IntensityData classes and their component classes
getY-method | Class IntensityData
getY-method | Class NcdfIntensityReader
gwasExactHW | Hardy-Weinberg Equilibrium testing
GWASTools | Tools for Genome Wide Association Studies
GWASTools-defunct | Defunct Functions in Package GWASTools

## -- H --

hasBAlleleFreq | Accessors for variables in GenotypeData and IntensityData classes and their component classes
hasBAlleleFreq-method | Class IntensityData
hasBAlleleFreq-method | Class NcdfIntensityReader
hasCoordVariable | Class NcdfReader
hasCoordVariable-method | Class NcdfReader
hasLogRRatio | Accessors for variables in GenotypeData and IntensityData classes and their component classes
hasLogRRatio-method | Class IntensityData
hasLogRRatio-method | Class NcdfIntensityReader
hasQuality | Accessors for variables in GenotypeData and IntensityData classes and their component classes
hasQuality-method | Class IntensityData
hasQuality-method | Class NcdfIntensityReader
hasScanAnnotation | Accessors for variables in GenotypeData and IntensityData classes and their component classes
hasScanAnnotation-method | Class GenotypeData
hasScanAnnotation-method | Class IntensityData
hasScanVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes
hasScanVariable-method | Class GenotypeData
hasScanVariable-method | Class IntensityData
hasSex | Accessors for variables in GenotypeData and IntensityData classes and their component classes
hasSex-method | Class GenotypeData
hasSex-method | Class IntensityData
hasSex-method | Class ScanAnotationDataFrame
hasSex-method | Class ScanAnotationSQLite
hasSnpAnnotation | Accessors for variables in GenotypeData and IntensityData classes and their component classes
hasSnpAnnotation-method | Class GenotypeData
hasSnpAnnotation-method | Class IntensityData
hasSnpVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes
hasSnpVariable-method | Class GenotypeData
hasSnpVariable-method | Class IntensityData
hasVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes
hasVariable-method | Class GdsReader
hasVariable-method | Class GenotypeData
hasVariable-method | Class IntensityData
hasVariable-method | Class NcdfReader
hasVariable-method | Class ScanAnotationDataFrame
hasVariable-method | Class ScanAnotationSQLite
hasVariable-method | Class SnpAnotationDataFrame
hasVariable-method | Class SnpAnotationSQLite
hasX | Accessors for variables in GenotypeData and IntensityData classes and their component classes
hasX-method | Class IntensityData
hasX-method | Class NcdfIntensityReader
hasY | Accessors for variables in GenotypeData and IntensityData classes and their component classes
hasY-method | Class IntensityData
hasY-method | Class NcdfIntensityReader
hetByScanChrom | Heterozygosity rates by scan and chromosome
hetBySnpSex | Heterozygosity by SNP and sex
HLA | HLA region base positions
HLA.hg18 | HLA region base positions
HLA.hg19 | HLA region base positions

## -- I --

ibdAreasDraw | Plot theoretical and observed identity by descent values and assign relationships
ibdAssignRelatedness | Plot theoretical and observed identity by descent values and assign relationships
ibdAssignRelatednessKing | Plot theoretical and observed identity by descent values and assign relationships
ibdPlot | Plot theoretical and observed identity by descent values and assign relationships
IntensityData | Class IntensityData
IntensityData-class | Class IntensityData
intensityOutliersPlot | Plot mean intensity and highlight outliers

## -- M --

manhattanPlot | Manhattan plot for genome wide association tests
MatrixGenotypeReader | Class MatrixGenotypeReader
MatrixGenotypeReader-class | Class MatrixGenotypeReader
MchromCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes
MchromCode-method | Class GdsGenotypeReader
MchromCode-method | Class GenotypeData
MchromCode-method | Class IntensityData
MchromCode-method | Class MatrixGenotypeReader
MchromCode-method | Class NcdfGenotypeReader
MchromCode-method | Class NcdfIntensityReader
MchromCode-method | Class SnpAnotationDataFrame
MchromCode-method | Class SnpAnotationSQLite
meanIntensityByScanChrom | Calculate Means & Standard Deviations of Intensities
meanSdByChromWindow | Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation
medianSdOverAutosomes | Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation
mendelErr | Mendelian Error Checking
mendelList | Mendelian Error Checking
mendelListAsDataFrame | Mendelian Error Checking
minorAlleleDetectionAccuracy | Duplicate discordance across datasets
missingGenotypeByScanChrom | Missing Counts per Scan per Chromosome
missingGenotypeBySnpSex | Missing Counts per SNP by Sex

## -- N --

ncdfAddData | Write genotypic calls and/or associated metrics to a netCDF file
ncdfAddIntensity | Write genotypic calls and/or associated metrics to a netCDF file
ncdfCheckGenotype | Write genotypic calls and/or associated metrics to a netCDF file
ncdfCheckIntensity | Write genotypic calls and/or associated metrics to a netCDF file
ncdfCreate | Write genotypic calls and/or associated metrics to a netCDF file.
NcdfGenotypeReader | Class NcdfGenotypeReader
NcdfGenotypeReader-class | Class NcdfGenotypeReader
ncdfImputedDosage | Create a NetCDF file with imputed dosages
NcdfIntensityReader | Class NcdfIntensityReader
NcdfIntensityReader-class | Class NcdfIntensityReader
NcdfReader | Class NcdfReader
NcdfReader-class | Class NcdfReader
ncdfSetMissingGenotypes | Write a new netCDF or GDS file, setting certain SNPs to missing
ncdfSubset | Write a subset of data in a netCDF file to a new netCDF file
ncdfSubsetCheck | Write a subset of data in a netCDF file to a new netCDF file
nscan | Accessors for variables in GenotypeData and IntensityData classes and their component classes
nscan-method | Class GdsGenotypeReader
nscan-method | Class GenotypeData
nscan-method | Class IntensityData
nscan-method | Class MatrixGenotypeReader
nscan-method | Class NcdfGenotypeReader
nscan-method | Class NcdfIntensityReader
nscan-method | Class ScanAnotationSQLite
nsnp | Accessors for variables in GenotypeData and IntensityData classes and their component classes
nsnp-method | Class GdsGenotypeReader
nsnp-method | Class GenotypeData
nsnp-method | Class IntensityData
nsnp-method | Class MatrixGenotypeReader
nsnp-method | Class NcdfGenotypeReader
nsnp-method | Class NcdfIntensityReader
nsnp-method | Class SnpAnotationSQLite

## -- O --

open-method | Class GdsReader
open-method | Class GenotypeData
open-method | Class IntensityData
open-method | Class NcdfReader
open-method | Class ScanAnotationSQLite
open-method | Class SnpAnotationSQLite

## -- P --

pcaSnpFilters | Regions of SNP-PC correlation to filter for Principal Component Analysis
pcaSnpFilters.hg18 | Regions of SNP-PC correlation to filter for Principal Component Analysis
pcaSnpFilters.hg19 | 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
plinkCheck | Utilities to create and check PLINK files
plinkToNcdf | Create a netCDF file and annotation suitable for use in GWASTools from PLINK files
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
pseudoautosomal.hg18 | Pseudoautosomal region base positions
pseudoautosomal.hg19 | Pseudoautosomal region base positions

## -- Q --

qqPlot | QQ plot for genome wide assocation studies
qualityScoreByScan | Mean and median quality score for scans
qualityScoreBySnp | Mean and median quality score for SNPs

## -- R --

readWriteFirst | Read and write the first n lines of a file
relationsMeanVar | Mean and Variance information for full-sibs, half-sibs, first-cousins

## -- S --

saveas | Save an R object with a new name
ScanAnnotationDataFrame | Class ScanAnotationDataFrame
ScanAnnotationDataFrame-class | Class ScanAnotationDataFrame
ScanAnnotationSQLite | Class ScanAnotationSQLite
ScanAnnotationSQLite-class | Class ScanAnotationSQLite
sdByScanChromWindow | Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation
show-method | Class GdsReader
show-method | Class GenotypeData
show-method | Class IntensityData
show-method | Class MatrixGenotypeReader
show-method | Class NcdfReader
show-method | Class ScanAnotationSQLite
show-method | Class SnpAnotationSQLite
simulateGenotypeMatrix | Simulate Genotype Matrix & Load into NetCDF File
simulateIntensityMatrix | Simulate Intensity Matrix & Load into NetCDF File
SnpAnnotationDataFrame | Class SnpAnotationDataFrame
SnpAnnotationDataFrame-class | Class SnpAnotationDataFrame
SnpAnnotationSQLite | Class SnpAnotationSQLite
SnpAnnotationSQLite-class | Class SnpAnotationSQLite
snpCorrelationPlot | SNP correlation plot

## -- W --

writeAnnotation | Accessors for variables in GenotypeData and IntensityData classes and their component classes
writeAnnotation-method | Class ScanAnotationSQLite
writeAnnotation-method | Class SnpAnotationSQLite
writeMetadata | Accessors for variables in GenotypeData and IntensityData classes and their component classes
writeMetadata-method | Class ScanAnotationSQLite
writeMetadata-method | Class SnpAnotationSQLite

## -- X --

XchromCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes
XchromCode-method | Class GdsGenotypeReader
XchromCode-method | Class GenotypeData
XchromCode-method | Class IntensityData
XchromCode-method | Class MatrixGenotypeReader
XchromCode-method | Class NcdfGenotypeReader
XchromCode-method | Class NcdfIntensityReader
XchromCode-method | Class SnpAnotationDataFrame
XchromCode-method | Class SnpAnotationSQLite
XYchromCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes
XYchromCode-method | Class GdsGenotypeReader
XYchromCode-method | Class GenotypeData
XYchromCode-method | Class IntensityData
XYchromCode-method | Class MatrixGenotypeReader
XYchromCode-method | Class NcdfGenotypeReader
XYchromCode-method | Class NcdfIntensityReader
XYchromCode-method | Class SnpAnotationDataFrame
XYchromCode-method | Class SnpAnotationSQLite

## -- Y --

YchromCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes
YchromCode-method | Class GdsGenotypeReader
YchromCode-method | Class GenotypeData
YchromCode-method | Class IntensityData
YchromCode-method | Class MatrixGenotypeReader
YchromCode-method | Class NcdfGenotypeReader
YchromCode-method | Class NcdfIntensityReader
YchromCode-method | Class SnpAnotationDataFrame
YchromCode-method | Class SnpAnotationSQLite