GWASTools: Tools for Genome Wide Association Studies

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.

AuthorStephanie M. Gogarten, Cathy Laurie, Tushar Bhangale, Matthew P. Conomos, Cecelia Laurie, Caitlin McHugh, Ian Painter, Xiuwen Zheng, Jess Shen, Rohit Swarnkar, Adrienne Stilp, Sarah Nelson
Date of publicationNone
MaintainerStephanie M. Gogarten <sdmorris@u.washington.edu>, Adrienne Stilp <amstilp@u.washington.edu>
LicenseArtistic-2.0
Version1.20.0

View on Bioconductor

Man pages

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

assocCoxPH: Cox proportional hazards

assocRegression: Association testing with regression

BAFfromClusterMeans: B Allele Frequency & Log R Ratio Calculation

BAFfromGenotypes: B Allele Frequency & Log R Ratio Calculation

batchTest: Batch Effects of Genotyping

centromeres: Centromere base positions

chromIntensityPlot: Plot B Allele Frequency and/or Log R Ratio, R or Theta values...

convertNcdfGds: Convert between NetCDF and GDS format

createDataFile: Write genotypic calls and/or associated metrics to a GDS or...

defunct: Defunct Functions in Package 'GWASTools'

duplicateDiscordance: Duplicate discordance

duplicateDiscordanceAcrossDatasets: Functions to check discordance and allelic dosage correlation...

duplicateDiscordanceProbability: Probability of duplicate discordance

exactHWE: Hardy-Weinberg Equilibrium testing

findBAFvariance: Find chromosomal areas with high BAlleleFreq (or LogRRatio)...

GdsGenotypeReader-class: Class GdsGenotypeReader

GdsIntensityReader-class: Class GdsIntensityReader

GdsReader-class: Class GdsReader

gdsSubset: Write a subset of data in a GDS file to a new GDS file

genoClusterPlot: SNP cluster plots

GenotypeData-class: Class GenotypeData

genotypeToCharacter: Convert number of A alleles to character genotypes

getobj: Get an R object stored in an Rdata file

getVariable: Accessors for variables in GenotypeData and IntensityData...

GWASTools-package: Tools for Genome Wide Association Studies

hetByScanChrom: Heterozygosity rates by scan and chromosome

hetBySnpSex: Heterozygosity by SNP and sex

HLA: HLA region base positions

ibdPlot: Plot theoretical and observed identity by descent values and...

imputedDosageFile: Create and check a GDS or NetCDF file with imputed dosages

IntensityData-class: Class IntensityData

intensityOutliersPlot: Plot mean intensity and highlight outliers

manhattanPlot: Manhattan plot for genome wide association tests

MatrixGenotypeReader-class: Class MatrixGenotypeReader

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

NcdfGenotypeReader-class: Class NcdfGenotypeReader

NcdfIntensityReader-class: Class NcdfIntensityReader

NcdfReader-class: Class NcdfReader

pasteSorted: Paste two vectors sorted pairwise

pcaSnpFilters: Regions of SNP-PC correlation to filter for Principal...

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...

pedigreePairwiseRelatedness: Assign relatedness from pedigree data

plinkUtils: Utilities to create and check PLINK files

pseudoautoIntensityPlot: Plot B Allele Frequency and Log R Ratio for the X and Y...

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,...

saveas: Save an R object with a new name

ScanAnnotationDataFrame-class: Class ScanAnotationDataFrame

ScanAnnotationSQLite-class: Class ScanAnotationSQLite

setMissingGenotypes: Write a new netCDF or GDS file, setting certain SNPs to...

simulateGenotypeMatrix: Simulate Genotype or Intensity Matrix & Load into GDS/NetCDF...

SnpAnnotationDataFrame-class: Class SnpAnotationDataFrame

SnpAnnotationSQLite-class: Class SnpAnotationSQLite

snpCorrelationPlot: SNP correlation plot

snpStats: Utilities for snpStats

vcfWrite: Utility to write VCF file

Functions

alleleFrequency Man page
allequal Man page
anomDetectBAF Man page
anomDetectLOH Man page
anomFilterBAF Man page
anomIdentifyLowQuality Man page
anomSegmentBAF Man page
anomSegStats Man page
anomStatsPlot Man page
apartSnpSelection Man page
asSnpMatrix Man page
assocCoxPH Man page
assocRegression Man page
assocTestCPH Man page
assocTestFisherExact Man page
assocTestRegression Man page
autosomeCode Man page
autosomeCode,GdsGenotypeReader-method Man page
autosomeCode,GdsIntensityReader-method Man page
autosomeCode,GenotypeData-method Man page
autosomeCode,IntensityData-method Man page
autosomeCode,MatrixGenotypeReader-method Man page
autosomeCode,NcdfGenotypeReader-method Man page
autosomeCode,NcdfIntensityReader-method Man page
autosomeCode,SnpAnnotationDataFrame-method Man page
autosomeCode,SnpAnnotationSQLite-method Man page
BAFfromClusterMeans Man page
BAFfromGenotypes Man page
batchChisqTest Man page
batchFisherTest Man page
centromeres Man page
centromeres.hg18 Man page
centromeres.hg19 Man page
centromeres.hg38 Man page
checkGenotypeFile Man page
checkImputedDosageFile Man page
checkIntensityFile Man page
checkNcdfGds Man page
chromIntensityPlot Man page
close,GdsReader-method Man page
close,GenotypeData-method Man page
close,IntensityData-method Man page
close,NcdfReader-method Man page
close,ScanAnnotationSQLite-method Man page
close,SnpAnnotationSQLite-method Man page
convertGdsNcdf Man page
convertNcdfGds Man page
convertVcfGds Man page
createAffyIntensityFile Man page
createDataFile Man page
dupDosageCorAcrossDatasets Man page
duplicateDiscordance Man page
duplicateDiscordanceAcrossDatasets Man page
duplicateDiscordanceProbability Man page
exactHWE Man page
findBAFvariance Man page
gdsCheckImputedDosage Man page
GdsGenotypeReader Man page
GdsGenotypeReader-class Man page
gdsImputedDosage Man page
GdsIntensityReader Man page
GdsIntensityReader-class Man page
GdsReader Man page
GdsReader-class Man page
gdsSetMissingGenotypes Man page
gdsSubset Man page
gdsSubsetCheck Man page
genoClusterPlot Man page
genoClusterPlotByBatch Man page
GenotypeData Man page
GenotypeData-class Man page
genotypeToCharacter Man page
getAlleleA Man page
getAlleleA,GdsGenotypeReader-method Man page
getAlleleA,GenotypeData-method Man page
getAlleleA,SnpAnnotationDataFrame-method Man page
getAlleleA,SnpAnnotationSQLite-method Man page
getAlleleB Man page
getAlleleB,GdsGenotypeReader-method Man page
getAlleleB,GenotypeData-method Man page
getAlleleB,SnpAnnotationDataFrame-method Man page
getAlleleB,SnpAnnotationSQLite-method Man page
getAnnotation Man page
getAnnotation,ScanAnnotationDataFrame-method Man page
getAnnotation,ScanAnnotationSQLite-method Man page
getAnnotation,SnpAnnotationDataFrame-method Man page
getAnnotation,SnpAnnotationSQLite-method Man page
getAttribute Man page
getAttribute,GdsReader-method Man page
getAttribute,NcdfReader-method Man page
getBAlleleFreq Man page
getBAlleleFreq,GdsIntensityReader-method Man page
getBAlleleFreq,IntensityData-method Man page
getBAlleleFreq,NcdfIntensityReader-method Man page
getChromosome Man page
getChromosome,GdsGenotypeReader-method Man page
getChromosome,GdsIntensityReader-method Man page
getChromosome,GenotypeData-method Man page
getChromosome,IntensityData-method Man page
getChromosome,MatrixGenotypeReader-method Man page
getChromosome,NcdfGenotypeReader-method Man page
getChromosome,NcdfIntensityReader-method Man page
getChromosome,SnpAnnotationDataFrame-method Man page
getChromosome,SnpAnnotationSQLite-method Man page
getDimension Man page
getDimension,GdsReader-method Man page
getDimensionNames Man page
getDimensionNames,NcdfReader-method Man page
getDimension,NcdfReader-method Man page
getGenotype Man page
getGenotype,GdsGenotypeReader-method Man page
getGenotype,GenotypeData-method Man page
getGenotype,MatrixGenotypeReader-method Man page
getGenotype,NcdfGenotypeReader-method Man page
getGenotypeSelection Man page
getGenotypeSelection,GdsGenotypeReader-method Man page
getGenotypeSelection,GenotypeData-method Man page
getGenotypeSelection,MatrixGenotypeReader-method Man page
getLogRRatio Man page
getLogRRatio,GdsIntensityReader-method Man page
getLogRRatio,IntensityData-method Man page
getLogRRatio,NcdfIntensityReader-method Man page
getMetadata Man page
getMetadata,ScanAnnotationDataFrame-method Man page
getMetadata,ScanAnnotationSQLite-method Man page
getMetadata,SnpAnnotationDataFrame-method Man page
getMetadata,SnpAnnotationSQLite-method Man page
getNodeDescription Man page
getNodeDescription,GdsReader-method Man page
getobj Man page
getPosition Man page
getPosition,GdsGenotypeReader-method Man page
getPosition,GdsIntensityReader-method Man page
getPosition,GenotypeData-method Man page
getPosition,IntensityData-method Man page
getPosition,MatrixGenotypeReader-method Man page
getPosition,NcdfGenotypeReader-method Man page
getPosition,NcdfIntensityReader-method Man page
getPosition,SnpAnnotationDataFrame-method Man page
getPosition,SnpAnnotationSQLite-method Man page
getQuality Man page
getQuality,GdsIntensityReader-method Man page
getQuality,IntensityData-method Man page
getQuality,NcdfIntensityReader-method Man page
getQuery Man page
getQuery,ScanAnnotationSQLite-method Man page
getQuery,SnpAnnotationSQLite-method Man page
getScanAnnotation Man page
getScanAnnotation,GenotypeData-method Man page
getScanID Man page
getScanID,GdsGenotypeReader-method Man page
getScanID,GdsIntensityReader-method Man page
getScanID,GenotypeData-method Man page
getScanID,IntensityData-method Man page
getScanID,MatrixGenotypeReader-method Man page
getScanID,NcdfGenotypeReader-method Man page
getScanID,NcdfIntensityReader-method Man page
getScanID,ScanAnnotationDataFrame-method Man page
getScanID,ScanAnnotationSQLite-method Man page
getScanVariable Man page
getScanVariable,GenotypeData-method Man page
getScanVariable,IntensityData-method Man page
getScanVariableNames Man page
getScanVariableNames,GenotypeData-method Man page
getScanVariableNames,IntensityData-method Man page
getSex Man page
getSex,GenotypeData-method Man page
getSex,IntensityData-method Man page
getSex,ScanAnnotationDataFrame-method Man page
getSex,ScanAnnotationSQLite-method Man page
getSnpAnnotation Man page
getSnpAnnotation,GenotypeData-method Man page
getSnpID Man page
getSnpID,GdsGenotypeReader-method Man page
getSnpID,GdsIntensityReader-method Man page
getSnpID,GenotypeData-method Man page
getSnpID,IntensityData-method Man page
getSnpID,MatrixGenotypeReader-method Man page
getSnpID,NcdfGenotypeReader-method Man page
getSnpID,NcdfIntensityReader-method Man page
getSnpID,SnpAnnotationDataFrame-method Man page
getSnpID,SnpAnnotationSQLite-method Man page
getSnpVariable Man page
getSnpVariable,GenotypeData-method Man page
getSnpVariable,IntensityData-method Man page
getSnpVariableNames Man page
getSnpVariableNames,GenotypeData-method Man page
getSnpVariableNames,IntensityData-method Man page
getVariable Man page
getVariable,GdsGenotypeReader-method Man page
getVariable,GdsIntensityReader-method Man page
getVariable,GdsReader-method Man page
getVariable,GenotypeData-method Man page
getVariable,IntensityData-method Man page
getVariableNames Man page
getVariableNames,GdsReader-method Man page
getVariableNames,NcdfReader-method Man page
getVariableNames,ScanAnnotationDataFrame-method Man page
getVariableNames,ScanAnnotationSQLite-method Man page
getVariableNames,SnpAnnotationDataFrame-method Man page
getVariableNames,SnpAnnotationSQLite-method Man page
getVariable,NcdfGenotypeReader-method Man page
getVariable,NcdfIntensityReader-method Man page
getVariable,NcdfReader-method Man page
getVariable,ScanAnnotationDataFrame-method Man page
getVariable,ScanAnnotationSQLite-method Man page
getVariable,SnpAnnotationDataFrame-method Man page
getVariable,SnpAnnotationSQLite-method Man page
getX Man page
getX,GdsIntensityReader-method Man page
getX,IntensityData-method Man page
getX,NcdfIntensityReader-method Man page
getY Man page
getY,GdsIntensityReader-method Man page
getY,IntensityData-method Man page
getY,NcdfIntensityReader-method Man page
gwasExactHW Man page
GWASTools Man page
GWASTools-defunct Man page
GWASTools-package Man page
hasBAlleleFreq Man page
hasBAlleleFreq,GdsIntensityReader-method Man page
hasBAlleleFreq,IntensityData-method Man page
hasBAlleleFreq,NcdfIntensityReader-method Man page
hasCoordVariable Man page
hasCoordVariable,NcdfReader-method Man page
hasLogRRatio Man page
hasLogRRatio,GdsIntensityReader-method Man page
hasLogRRatio,IntensityData-method Man page
hasLogRRatio,NcdfIntensityReader-method Man page
hasQuality Man page
hasQuality,GdsIntensityReader-method Man page
hasQuality,IntensityData-method Man page
hasQuality,NcdfIntensityReader-method Man page
hasScanAnnotation Man page
hasScanAnnotation,GenotypeData-method Man page
hasScanAnnotation,IntensityData-method Man page
hasScanVariable Man page
hasScanVariable,GenotypeData-method Man page
hasScanVariable,IntensityData-method Man page
hasSex Man page
hasSex,GenotypeData-method Man page
hasSex,IntensityData-method Man page
hasSex,ScanAnnotationDataFrame-method Man page
hasSex,ScanAnnotationSQLite-method Man page
hasSnpAnnotation Man page
hasSnpAnnotation,GenotypeData-method Man page
hasSnpAnnotation,IntensityData-method Man page
hasSnpVariable Man page
hasSnpVariable,GenotypeData-method Man page
hasSnpVariable,IntensityData-method Man page
hasVariable Man page
hasVariable,GdsReader-method Man page
hasVariable,GenotypeData-method Man page
hasVariable,IntensityData-method Man page
hasVariable,NcdfReader-method Man page
hasVariable,ScanAnnotationDataFrame-method Man page
hasVariable,ScanAnnotationSQLite-method Man page
hasVariable,SnpAnnotationDataFrame-method Man page
hasVariable,SnpAnnotationSQLite-method Man page
hasX Man page
hasX,GdsIntensityReader-method Man page
hasX,IntensityData-method Man page
hasX,NcdfIntensityReader-method Man page
hasY Man page
hasY,GdsIntensityReader-method Man page
hasY,IntensityData-method Man page
hasY,NcdfIntensityReader-method Man page
hetByScanChrom Man page
hetBySnpSex Man page
HLA Man page
HLA.hg18 Man page
HLA.hg19 Man page
HLA.hg38 Man page
ibdAreasDraw Man page
ibdAssignRelatedness Man page
ibdAssignRelatednessKing Man page
ibdPlot Man page
imputedDosageFile Man page
IntensityData Man page
IntensityData-class Man page
intensityOutliersPlot Man page
kingIBS0FSCI Man page
manhattanPlot Man page
MatrixGenotypeReader Man page
MatrixGenotypeReader-class Man page
MchromCode Man page
MchromCode,GdsGenotypeReader-method Man page
MchromCode,GdsIntensityReader-method Man page
MchromCode,GenotypeData-method Man page
MchromCode,IntensityData-method Man page
MchromCode,MatrixGenotypeReader-method Man page
MchromCode,NcdfGenotypeReader-method Man page
MchromCode,NcdfIntensityReader-method Man page
MchromCode,SnpAnnotationDataFrame-method Man page
MchromCode,SnpAnnotationSQLite-method Man page
meanIntensityByScanChrom Man page
meanSdByChromWindow Man page
medianSdOverAutosomes Man page
mendelErr Man page
mendelList Man page
mendelListAsDataFrame Man page
minorAlleleDetectionAccuracy Man page
missingGenotypeByScanChrom Man page
missingGenotypeBySnpSex Man page
ncdfAddData Man page
ncdfAddIntensity Man page
ncdfCheckGenotype Man page
ncdfCheckIntensity Man page
ncdfCreate Man page
NcdfGenotypeReader Man page
NcdfGenotypeReader-class Man page
ncdfImputedDosage Man page
NcdfIntensityReader Man page
NcdfIntensityReader-class Man page
NcdfReader Man page
NcdfReader-class Man page
ncdfSetMissingGenotypes Man page
ncdfSubset Man page
ncdfSubsetCheck Man page
nscan Man page
nscan,GdsGenotypeReader-method Man page
nscan,GdsIntensityReader-method Man page
nscan,GenotypeData-method Man page
nscan,IntensityData-method Man page
nscan,MatrixGenotypeReader-method Man page
nscan,NcdfGenotypeReader-method Man page
nscan,NcdfIntensityReader-method Man page
nscan,ScanAnnotationSQLite-method Man page
nsnp Man page
nsnp,GdsGenotypeReader-method Man page
nsnp,GdsIntensityReader-method Man page
nsnp,GenotypeData-method Man page
nsnp,IntensityData-method Man page
nsnp,MatrixGenotypeReader-method Man page
nsnp,NcdfGenotypeReader-method Man page
nsnp,NcdfIntensityReader-method Man page
nsnp,SnpAnnotationSQLite-method Man page
open,GdsReader-method Man page
open,GenotypeData-method Man page
open,IntensityData-method Man page
open,NcdfReader-method Man page
open,ScanAnnotationSQLite-method Man page
open,SnpAnnotationSQLite-method Man page
pasteSorted Man page
pcaSnpFilters Man page
pcaSnpFilters.hg18 Man page
pcaSnpFilters.hg19 Man page
pcaSnpFilters.hg38 Man page
pedigreeCheck Man page
pedigreeDeleteDuplicates Man page
pedigreeMaxUnrelated Man page
pedigreePairwiseRelatedness Man page
plinkCheck Man page
plinkToNcdf Man page
plinkWrite Man page
pseudoautoIntensityPlot Man page
pseudoautosomal Man page
pseudoautosomal.hg18 Man page
pseudoautosomal.hg19 Man page
pseudoautosomal.hg38 Man page
qqPlot Man page
qualityScoreByScan Man page
qualityScoreBySnp Man page
readWriteFirst Man page
relationsMeanVar Man page
saveas Man page
ScanAnnotationDataFrame Man page
ScanAnnotationDataFrame-class Man page
ScanAnnotationSQLite Man page
ScanAnnotationSQLite-class Man page
sdByScanChromWindow Man page
setMissingGenotypes Man page
show,GdsReader-method Man page
show,GenotypeData-method Man page
show,IntensityData-method Man page
show,MatrixGenotypeReader-method Man page
show,NcdfReader-method Man page
show,ScanAnnotationSQLite-method Man page
show,SnpAnnotationSQLite-method Man page
simulateGenotypeMatrix Man page
simulateIntensityMatrix Man page
SnpAnnotationDataFrame Man page
SnpAnnotationDataFrame-class Man page
SnpAnnotationSQLite Man page
SnpAnnotationSQLite-class Man page
snpCorrelationPlot Man page
vcfCheck Man page
vcfWrite Man page
writeAnnotation Man page
writeAnnotation,ScanAnnotationSQLite-method Man page
writeAnnotation,SnpAnnotationSQLite-method Man page
writeMetadata Man page
writeMetadata,ScanAnnotationSQLite-method Man page
writeMetadata,SnpAnnotationSQLite-method Man page
XchromCode Man page
XchromCode,GdsGenotypeReader-method Man page
XchromCode,GdsIntensityReader-method Man page
XchromCode,GenotypeData-method Man page
XchromCode,IntensityData-method Man page
XchromCode,MatrixGenotypeReader-method Man page
XchromCode,NcdfGenotypeReader-method Man page
XchromCode,NcdfIntensityReader-method Man page
XchromCode,SnpAnnotationDataFrame-method Man page
XchromCode,SnpAnnotationSQLite-method Man page
XYchromCode Man page
XYchromCode,GdsGenotypeReader-method Man page
XYchromCode,GdsIntensityReader-method Man page
XYchromCode,GenotypeData-method Man page
XYchromCode,IntensityData-method Man page
XYchromCode,MatrixGenotypeReader-method Man page
XYchromCode,NcdfGenotypeReader-method Man page
XYchromCode,NcdfIntensityReader-method Man page
XYchromCode,SnpAnnotationDataFrame-method Man page
XYchromCode,SnpAnnotationSQLite-method Man page
YchromCode Man page
YchromCode,GdsGenotypeReader-method Man page
YchromCode,GdsIntensityReader-method Man page
YchromCode,GenotypeData-method Man page
YchromCode,IntensityData-method Man page
YchromCode,MatrixGenotypeReader-method Man page
YchromCode,NcdfGenotypeReader-method Man page
YchromCode,NcdfIntensityReader-method Man page
YchromCode,SnpAnnotationDataFrame-method Man page
YchromCode,SnpAnnotationSQLite-method Man page

Files

GWASTools/DESCRIPTION
GWASTools/NAMESPACE
GWASTools/R
GWASTools/R/AllClasses.R GWASTools/R/AllGenerics.R GWASTools/R/BAFfromClusterMeans.R GWASTools/R/BAFfromGenotypes.R GWASTools/R/LOHfind.R GWASTools/R/LOHselectAnoms.R GWASTools/R/Methods-GdsGenotypeReader.R GWASTools/R/Methods-GdsIntensityReader.R GWASTools/R/Methods-GdsReader.R GWASTools/R/Methods-GenotypeData.R GWASTools/R/Methods-IntensityData.R GWASTools/R/Methods-MatrixGenotypeReader.R GWASTools/R/Methods-NcdfGenotypeReader.R GWASTools/R/Methods-NcdfIntensityReader.R GWASTools/R/Methods-NcdfReader.R GWASTools/R/Methods-ScanAnnotationDataFrame.R GWASTools/R/Methods-ScanAnnotationSQLite.R GWASTools/R/Methods-SnpAnnotationDataFrame.R GWASTools/R/Methods-SnpAnnotationSQLite.R GWASTools/R/alleleFrequency.R GWASTools/R/anomDetectBAF.R GWASTools/R/anomDetectLOH.R GWASTools/R/anomFilterBAF.R GWASTools/R/anomIdentifyLowQuality.R GWASTools/R/anomSegStats.R GWASTools/R/anomSegmentBAF.R GWASTools/R/anomStatsPlot.R GWASTools/R/apartSnpSelection.R GWASTools/R/assocCoxPH.R GWASTools/R/assocRegression.R GWASTools/R/batchChisqTest.R GWASTools/R/batchFisherTest.R GWASTools/R/checkGenotypeFile.R GWASTools/R/checkImputedDosageFile.R GWASTools/R/checkIntensityFile.R GWASTools/R/chromIntensityPlot.R GWASTools/R/convertNcdfGds.R GWASTools/R/createAffyIntensityFile.R GWASTools/R/createDataFile.R GWASTools/R/createDataUtils.R GWASTools/R/defunct.R GWASTools/R/dupDosageCorAcrossDatasets.R GWASTools/R/duplicateDiscordance.R GWASTools/R/duplicateDiscordanceAcrossDatasets.R GWASTools/R/duplicateDiscordanceProbability.R GWASTools/R/exactHWE.R GWASTools/R/findBAFvariance.R GWASTools/R/findRelationsMeanVar.R GWASTools/R/gdsSubset.R GWASTools/R/gdsSubsetCheck.R GWASTools/R/genoClusterPlot.R GWASTools/R/genoClusterPlotByBatch.R GWASTools/R/genotypeToCharacter.R GWASTools/R/hetByScanChrom.R GWASTools/R/hetBySnpSex.R GWASTools/R/ibdAreasDraw.R GWASTools/R/ibdAssignRelatedness.R GWASTools/R/ibdPlot.R GWASTools/R/imputedDosageFile.R GWASTools/R/intensityOutliersPlot.R GWASTools/R/manhattanPlot.R GWASTools/R/meanIntensityByScanChrom.R GWASTools/R/meanSdByChromWindow.R GWASTools/R/medianSdOverAutosomes.R GWASTools/R/mendelErr.R GWASTools/R/missingGenotypeByScanChrom.R GWASTools/R/missingGenotypeBySnpSex.R GWASTools/R/pedigreeCheck.R GWASTools/R/pedigreeDeleteDuplicates.R GWASTools/R/pedigreeMaxUnrelated.R GWASTools/R/pedigreePairwiseRelatedness.R GWASTools/R/plinkUtils.R GWASTools/R/pseudoautoIntensityPlot.R GWASTools/R/qqPlot.R GWASTools/R/qualityScoreByScan.R GWASTools/R/qualityScoreBySnp.R GWASTools/R/sdByScanChromWindow.R GWASTools/R/setMissingGenotypes.R GWASTools/R/simulateGenotypeMatrix.R GWASTools/R/simulateIntensityMatrix.R GWASTools/R/snpCorrelationPlot.R GWASTools/R/snpStats.R GWASTools/R/utils.R GWASTools/R/vcfWrite.R
GWASTools/build
GWASTools/build/vignette.rds
GWASTools/data
GWASTools/data/HLA.hg18.RData
GWASTools/data/HLA.hg19.RData
GWASTools/data/HLA.hg38.RData
GWASTools/data/centromeres.hg18.RData
GWASTools/data/centromeres.hg19.RData
GWASTools/data/centromeres.hg38.RData
GWASTools/data/pcaSnpFilters.hg18.RData
GWASTools/data/pcaSnpFilters.hg19.RData
GWASTools/data/pcaSnpFilters.hg38.RData
GWASTools/data/pseudoautosomal.hg18.RData
GWASTools/data/pseudoautosomal.hg19.RData
GWASTools/data/pseudoautosomal.hg38.RData
GWASTools/data/relationsMeanVar.RData
GWASTools/inst
GWASTools/inst/CITATION
GWASTools/inst/NEWS.Rd
GWASTools/inst/doc
GWASTools/inst/doc/Affymetrix.R
GWASTools/inst/doc/Affymetrix.Rnw
GWASTools/inst/doc/Affymetrix.pdf
GWASTools/inst/doc/DataCleaning.R
GWASTools/inst/doc/DataCleaning.Rnw
GWASTools/inst/doc/DataCleaning.pdf
GWASTools/inst/doc/Formats.R
GWASTools/inst/doc/Formats.Rnw
GWASTools/inst/doc/Formats.pdf
GWASTools/inst/unitTests
GWASTools/inst/unitTests/BAFfromClusterMeans_test.R
GWASTools/inst/unitTests/BAFfromGenotypes_test.R
GWASTools/inst/unitTests/GdsGenotypeReader_test.R
GWASTools/inst/unitTests/GdsIntensityReader_test.R
GWASTools/inst/unitTests/GdsReader_test.R
GWASTools/inst/unitTests/GenotypeData_test.R
GWASTools/inst/unitTests/IntensityData_test.R
GWASTools/inst/unitTests/MatrixGenotypeReader_test.R
GWASTools/inst/unitTests/NcdfGenotypeReader_test.R
GWASTools/inst/unitTests/NcdfIntensityReader_test.R
GWASTools/inst/unitTests/NcdfReader_test.R
GWASTools/inst/unitTests/ScanAnnotationDataFrame_test.R
GWASTools/inst/unitTests/ScanAnnotationSQLite_test.R
GWASTools/inst/unitTests/SnpAnnotationDataFrame_test.R
GWASTools/inst/unitTests/SnpAnnotationSQLite_test.R
GWASTools/inst/unitTests/alleleFrequency_test.R
GWASTools/inst/unitTests/allequal_test.R
GWASTools/inst/unitTests/anomDetectBAF_test.R
GWASTools/inst/unitTests/apartSnpSelection_test.R
GWASTools/inst/unitTests/assocCoxPH_test.R
GWASTools/inst/unitTests/assocRegression_test.R
GWASTools/inst/unitTests/batchChisqTest_test.R
GWASTools/inst/unitTests/batchFisherTest_test.R
GWASTools/inst/unitTests/checkGenotypeFile_test.R
GWASTools/inst/unitTests/checkImputedDosageFile_test.R
GWASTools/inst/unitTests/checkIntensityFile_test.R
GWASTools/inst/unitTests/chromIntensityPlot_test.R
GWASTools/inst/unitTests/convertNcdfGds_test.R
GWASTools/inst/unitTests/createAffyIntensityFile_test.R
GWASTools/inst/unitTests/createDataFile_test.R
GWASTools/inst/unitTests/dupDosageCorAcrossDatasets_test.R
GWASTools/inst/unitTests/duplicateDiscordanceAcrossDatasets_test.R
GWASTools/inst/unitTests/duplicateDiscordance_test.R
GWASTools/inst/unitTests/exactHWE_test.R
GWASTools/inst/unitTests/findBAFvariance_test.R
GWASTools/inst/unitTests/gdsSubsetCheck_test.R
GWASTools/inst/unitTests/gdsSubset_test.R
GWASTools/inst/unitTests/genotypeToCharacter_test.R
GWASTools/inst/unitTests/getobj_test.R
GWASTools/inst/unitTests/hetByScanChrom_test.R
GWASTools/inst/unitTests/hetBySnpSex_test.R
GWASTools/inst/unitTests/ibdPlot_test.R
GWASTools/inst/unitTests/imputedDosageFile_test.R
GWASTools/inst/unitTests/meanIntensityByScanChrom_test.R
GWASTools/inst/unitTests/missingGenotypeByScanChrom_test.R
GWASTools/inst/unitTests/missingGenotypeBySnpSex_test.R
GWASTools/inst/unitTests/pedigreeCheck_test.R
GWASTools/inst/unitTests/pedigreeMaxUnrelated_test.R
GWASTools/inst/unitTests/pedigreePairwiseRelatedness_test.R
GWASTools/inst/unitTests/plinkUtils_test.R
GWASTools/inst/unitTests/pseudoautoIntensityPlot_test.R
GWASTools/inst/unitTests/qualityScoreByScan_test.R
GWASTools/inst/unitTests/qualityScoreBySnp_test.R
GWASTools/inst/unitTests/saveas_test.R
GWASTools/inst/unitTests/setMissingGenotypes_test.R
GWASTools/inst/unitTests/snpStats_test.R
GWASTools/inst/unitTests/vcfWrite_test.R
GWASTools/man
GWASTools/man/BAFfromClusterMeans.Rd GWASTools/man/BAFfromGenotypes.Rd GWASTools/man/GWASTools-package.Rd GWASTools/man/GdsGenotypeReader-class.Rd GWASTools/man/GdsIntensityReader-class.Rd GWASTools/man/GdsReader-class.Rd GWASTools/man/GenotypeData-class.Rd GWASTools/man/HLA.Rd GWASTools/man/IntensityData-class.Rd GWASTools/man/MatrixGenotypeReader-class.Rd GWASTools/man/NcdfGenotypeReader-class.Rd GWASTools/man/NcdfIntensityReader-class.Rd GWASTools/man/NcdfReader-class.Rd GWASTools/man/ScanAnnotationDataFrame-class.Rd GWASTools/man/ScanAnnotationSQLite-class.Rd GWASTools/man/SnpAnnotationDataFrame-class.Rd GWASTools/man/SnpAnnotationSQLite-class.Rd GWASTools/man/alleleFrequency.Rd GWASTools/man/allequal.Rd GWASTools/man/anomDetectBAF.Rd GWASTools/man/anomDetectLOH.Rd GWASTools/man/anomIdentifyLowQuality.Rd GWASTools/man/anomSegStats.Rd GWASTools/man/apartSnpSelection.Rd GWASTools/man/assocCoxPH.Rd GWASTools/man/assocRegression.Rd GWASTools/man/batchTest.Rd GWASTools/man/centromeres.Rd GWASTools/man/chromIntensityPlot.Rd GWASTools/man/convertNcdfGds.Rd GWASTools/man/createDataFile.Rd GWASTools/man/defunct.Rd GWASTools/man/duplicateDiscordance.Rd GWASTools/man/duplicateDiscordanceAcrossDatasets.Rd GWASTools/man/duplicateDiscordanceProbability.Rd GWASTools/man/exactHWE.Rd GWASTools/man/findBAFvariance.Rd GWASTools/man/gdsSubset.Rd GWASTools/man/genoClusterPlot.Rd GWASTools/man/genotypeToCharacter.Rd GWASTools/man/getVariable.Rd GWASTools/man/getobj.Rd GWASTools/man/hetByScanChrom.Rd GWASTools/man/hetBySnpSex.Rd GWASTools/man/ibdPlot.Rd GWASTools/man/imputedDosageFile.Rd GWASTools/man/intensityOutliersPlot.Rd GWASTools/man/manhattanPlot.Rd GWASTools/man/meanIntensityByScanChrom.Rd GWASTools/man/mendelErr.Rd GWASTools/man/mendelList.Rd GWASTools/man/missingGenotypeByScanChrom.Rd GWASTools/man/missingGenotypeBySnpSex.Rd GWASTools/man/pasteSorted.Rd GWASTools/man/pcaSnpFilters.Rd GWASTools/man/pedigreeCheck.Rd GWASTools/man/pedigreeDeleteDuplicates.Rd GWASTools/man/pedigreeMaxUnrelated.Rd GWASTools/man/pedigreePairwiseRelatedness.Rd GWASTools/man/plinkUtils.Rd GWASTools/man/pseudoautoIntensityPlot.Rd GWASTools/man/pseudoautosomal.Rd GWASTools/man/qqPlot.Rd GWASTools/man/qualityScoreByScan.Rd GWASTools/man/qualityScoreBySnp.Rd GWASTools/man/readWriteFirst.Rd GWASTools/man/relationsMeanVar.Rd GWASTools/man/saveas.Rd GWASTools/man/setMissingGenotypes.Rd GWASTools/man/simulateGenotypeMatrix.Rd GWASTools/man/snpCorrelationPlot.Rd GWASTools/man/snpStats.Rd GWASTools/man/vcfWrite.Rd
GWASTools/tests
GWASTools/tests/test.R
GWASTools/vignettes
GWASTools/vignettes/Affymetrix.Rnw
GWASTools/vignettes/DataCleaning.Rnw
GWASTools/vignettes/Formats.Rnw

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