GWASTools: Tools for Genome Wide Association Studies
Version 1.22.0

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
Bioconductor views GeneticVariability Microarray QualityControl SNP
Date of publicationNone
MaintainerStephanie M. Gogarten <sdmorris@u.washington.edu>, Adrienne Stilp <amstilp@u.washington.edu>
LicenseArtistic-2.0
Version1.22.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GWASTools")

Getting started

Package overview

Popular man pages

assocCoxPH: Cox proportional hazards
BAFfromClusterMeans: B Allele Frequency & Log R Ratio Calculation
chromIntensityPlot: Plot B Allele Frequency and/or Log R Ratio, R or Theta values...
GWASTools-package: Tools for Genome Wide Association Studies
hetByScanChrom: Heterozygosity rates by scan and chromosome
mendelErr: Mendelian Error Checking
pseudoautoIntensityPlot: Plot B Allele Frequency and Log R Ratio for the X and Y...
See all...

All man pages Function index File listing

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

BAFfromClusterMeans Man page Source code
BAFfromGenotypes Man page Source code
CI Source code
GWASTools Man page
GWASTools-defunct Man page
GWASTools-package Man page
GdsGenotypeReader Man page Source code
GdsGenotypeReader-class Man page
GdsIntensityReader Man page Source code
GdsIntensityReader-class Man page
GdsReader Man page Source code
GdsReader-class Man page
GenotypeData Man page Source code
GenotypeData-class Man page
HLA Man page
HLA.hg18 Man page
HLA.hg19 Man page
HLA.hg38 Man page
IntensityData Man page Source code
IntensityData-class Man page
MatrixGenotypeReader Man page Source code
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
NcdfGenotypeReader Man page Source code
NcdfGenotypeReader-class Man page
NcdfIntensityReader Man page Source code
NcdfIntensityReader-class Man page
NcdfReader Man page Source code
NcdfReader-class Man page
OHbase Source code
OHfind Source code
OHlocalMad Source code
OHruns Source code
OHselectAnoms Source code
ScanAnnotationDataFrame Man page Source code
ScanAnnotationDataFrame-class Man page
ScanAnnotationSQLite Man page Source code
ScanAnnotationSQLite-class Man page
SnpAnnotationDataFrame Man page Source code
SnpAnnotationDataFrame-class Man page
SnpAnnotationSQLite Man page Source code
SnpAnnotationSQLite-class 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
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
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
addChromosomeAttributes Source code
addData Source code
addData.gds.class Source code
addData.ncdf4 Source code
addDataBySnp Source code
addDataBySnp.gds.class Source code
addDataBySnp.ncdf4 Source code
addDosage Source code
addDosage.gds.class Source code
addDosage.ncdf4 Source code
addNamesGds Source code
addNamesNcdf Source code
addSnpVars Source code
addSnpVars.gds.class Source code
addSnpVars.ncdf4 Source code
alleleFrequency Man page Source code
allequal Man page Source code
anomDetectBAF Man page Source code
anomDetectLOH Man page Source code
anomFilterBAF Man page Source code
anomIdentifyLowQuality Man page Source code
anomSegStats Man page Source code
anomSegmentBAF Man page Source code
anomStatsPlot Man page Source code
apartSnpSelection Man page Source code
asSnpMatrix Man page Source code
assocCoxPH Man page Source code
assocRegression Man page Source code
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
batchChisqTest Man page Source code
batchFisherTest Man page Source code
batchGenotypeCounts Source code
batchSexCheck Source code
batchSnpInclude Source code
centromeres Man page
centromeres.hg18 Man page
centromeres.hg19 Man page
centromeres.hg38 Man page
checkGenotypeFile Man page Source code
checkImputedDosageFile Man page Source code
checkIntensityFile Man page Source code
checkNameCols Source code
checkNcdfGds Man page Source code
checkSexChr Source code
checkSexChrHWE Source code
checkSnpAnnotation Source code
checkVars Source code
chromIntensityPlot Man page Source code
close Source code
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
close.gds.class Source code
close.ncdf4 Source code
colorByGeno Source code
commonSnps Source code
compressDosage Source code
convertGdsNcdf Man page Source code
convertNcdfGds Man page Source code
convertVcfGds Man page
countGenotypes Source code
createAffyIntensityFile Man page Source code
createDataFile Man page Source code
createGds Source code
createGdsBySnp Source code
createGdsDosage Source code
createNcdf Source code
createNcdfDosage Source code
delHomoRuns Source code
dentifyLowQual Source code
discordantPair Source code
dosCorSelectGenotype Source code
dupDosageCorAcrossDatasets Man page Source code
duplicateDiscordance Man page Source code
duplicateDiscordanceAcrossDatasets Man page Source code
duplicateDiscordanceProbability Man page Source code
duplicatePairs Source code
exactHWE Man page Source code
falseNeg Source code
falsePos Source code
findBAFvariance Man page Source code
freqFromGeno Source code
gdsCheckImputedDosage Man page
gdsImputedDosage Man page
gdsSetMissingGenotypes Man page
gdsSubset Man page Source code
gdsSubsetCheck Man page Source code
genoAsInt Source code
genoClass Source code
genoClusterPlot Man page Source code
genoClusterPlotByBatch Man page Source code
genotypeToCharacter Man page Source code
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
getBatch Source code
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
getDimension,NcdfReader-method Man page
getDimensionNames Man page
getDimensionNames,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 Source code
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
getPlinkFam Source code
getPlinkGenotype Source code
getPlinkMap Source code
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
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
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
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
getobj Man page Source code
gwasExactHW 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 Source code
hetBySnpSex Man page Source code
ibdAreasDraw Man page Source code
ibdAssignRelatedness Man page Source code
ibdAssignRelatednessKing Man page Source code
ibdPlot Man page Source code
imputedDosageFile Man page Source code
intensityOutliersPlot Man page Source code
keepSamples Source code
kingIBS0FSCI Man page Source code
logicalIndex Source code
majorGenotype Source code
manhattanPlot Man page Source code
mapAlleles Source code
meanIntensityByScanChrom Man page Source code
meanSdByChromWindow Man page Source code
medianSdOverAutosomes Man page Source code
mendelErr Man page Source code
mendelList Man page Source code
mendelListAsDataFrame Man page Source code
mergeSeg Source code
minExpFreq Source code
minorAlleleDetectionAccuracy Man page Source code
missingGenotypeByScanChrom Man page Source code
missingGenotypeBySnpSex Man page Source code
mmerge Source code
modelData Source code
monomorphic Source code
ncdfAddData Man page
ncdfAddIntensity Man page
ncdfCheckGenotype Man page
ncdfCheckIntensity Man page
ncdfCreate Man page
ncdfImputedDosage Man page
ncdfSetMissingGenotypes Man page
ncdfSubset Man page
ncdfSubsetCheck Man page
nitialChecks Source code
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
orderBySelection Source code
pasteSorted Man page Source code
pcaSnpFilters Man page
pcaSnpFilters.hg18 Man page
pcaSnpFilters.hg19 Man page
pcaSnpFilters.hg38 Man page
pedigreeCheck Man page Source code
pedigreeDeleteDuplicates Man page Source code
pedigreeMaxUnrelated Man page Source code
pedigreePairwiseRelatedness Man page Source code
permuteGenotypes Source code
permuteGenotypesSlow Source code
phi Source code
plinkCheck Man page Source code
plinkToNcdf Man page
plinkWrite Man page Source code
probToDosage Source code
probToGenotype Source code
pseudoautoIntensityPlot Man page Source code
pseudoautosomal Man page
pseudoautosomal.hg18 Man page
pseudoautosomal.hg19 Man page
pseudoautosomal.hg38 Man page
qqPlot Man page Source code
qualityScoreByScan Man page Source code
qualityScoreBySnp Man page Source code
readWriteFirst Man page Source code
relate Source code
relationsMeanVar Man page
reopenGds Source code
returnSnpScan Source code
runCPH Source code
runFirth Source code
runRegression Source code
runsMerge Source code
sampCharac Source code
saveas Man page Source code
sdByScanChromWindow Man page Source code
selectGenotype Source code
setFilter Source code
setInfo Source code
setMissingGenotypes Man page Source code
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 Source code
simulateIntensityMatrix Man page Source code
snpCorrelationPlot Man page Source code
startCountToIndex Source code
transformGenotype Source code
trueNeg Source code
truePos Source code
vcfCheck Man page Source code
vcfWrite Man page Source code
waldTest Source code
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
zoom2 Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/BAFfromClusterMeans.R
R/BAFfromGenotypes.R
R/LOHfind.R
R/LOHselectAnoms.R
R/Methods-GdsGenotypeReader.R
R/Methods-GdsIntensityReader.R
R/Methods-GdsReader.R
R/Methods-GenotypeData.R
R/Methods-IntensityData.R
R/Methods-MatrixGenotypeReader.R
R/Methods-NcdfGenotypeReader.R
R/Methods-NcdfIntensityReader.R
R/Methods-NcdfReader.R
R/Methods-ScanAnnotationDataFrame.R
R/Methods-ScanAnnotationSQLite.R
R/Methods-SnpAnnotationDataFrame.R
R/Methods-SnpAnnotationSQLite.R
R/alleleFrequency.R
R/anomDetectBAF.R
R/anomDetectLOH.R
R/anomFilterBAF.R
R/anomIdentifyLowQuality.R
R/anomSegStats.R
R/anomSegmentBAF.R
R/anomStatsPlot.R
R/apartSnpSelection.R
R/assocCoxPH.R
R/assocRegression.R
R/batchChisqTest.R
R/batchFisherTest.R
R/checkGenotypeFile.R
R/checkImputedDosageFile.R
R/checkIntensityFile.R
R/chromIntensityPlot.R
R/convertNcdfGds.R
R/createAffyIntensityFile.R
R/createDataFile.R
R/createDataUtils.R
R/dupDosageCorAcrossDatasets.R
R/duplicateDiscordance.R
R/duplicateDiscordanceAcrossDatasets.R
R/duplicateDiscordanceProbability.R
R/exactHWE.R
R/findBAFvariance.R
R/findRelationsMeanVar.R
R/gdsSubset.R
R/gdsSubsetCheck.R
R/genoClusterPlot.R
R/genoClusterPlotByBatch.R
R/genotypeToCharacter.R
R/hetByScanChrom.R
R/hetBySnpSex.R
R/ibdAreasDraw.R
R/ibdAssignRelatedness.R
R/ibdPlot.R
R/imputedDosageFile.R
R/intensityOutliersPlot.R
R/manhattanPlot.R
R/meanIntensityByScanChrom.R
R/meanSdByChromWindow.R
R/medianSdOverAutosomes.R
R/mendelErr.R
R/missingGenotypeByScanChrom.R
R/missingGenotypeBySnpSex.R
R/pedigreeCheck.R
R/pedigreeDeleteDuplicates.R
R/pedigreeMaxUnrelated.R
R/pedigreePairwiseRelatedness.R
R/plinkUtils.R
R/pseudoautoIntensityPlot.R
R/qqPlot.R
R/qualityScoreByScan.R
R/qualityScoreBySnp.R
R/sdByScanChromWindow.R
R/setMissingGenotypes.R
R/simulateGenotypeMatrix.R
R/simulateIntensityMatrix.R
R/snpCorrelationPlot.R
R/snpStats.R
R/utils.R
R/vcfWrite.R
build
build/vignette.rds
data
data/HLA.hg18.RData
data/HLA.hg19.RData
data/HLA.hg38.RData
data/centromeres.hg18.RData
data/centromeres.hg19.RData
data/centromeres.hg38.RData
data/pcaSnpFilters.hg18.RData
data/pcaSnpFilters.hg19.RData
data/pcaSnpFilters.hg38.RData
data/pseudoautosomal.hg18.RData
data/pseudoautosomal.hg19.RData
data/pseudoautosomal.hg38.RData
data/relationsMeanVar.RData
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/Affymetrix.R
inst/doc/Affymetrix.Rnw
inst/doc/Affymetrix.pdf
inst/doc/DataCleaning.R
inst/doc/DataCleaning.Rnw
inst/doc/DataCleaning.pdf
inst/doc/Formats.R
inst/doc/Formats.Rnw
inst/doc/Formats.pdf
inst/unitTests
inst/unitTests/BAFfromClusterMeans_test.R
inst/unitTests/BAFfromGenotypes_test.R
inst/unitTests/GdsGenotypeReader_test.R
inst/unitTests/GdsIntensityReader_test.R
inst/unitTests/GdsReader_test.R
inst/unitTests/GenotypeData_test.R
inst/unitTests/IntensityData_test.R
inst/unitTests/MatrixGenotypeReader_test.R
inst/unitTests/NcdfGenotypeReader_test.R
inst/unitTests/NcdfIntensityReader_test.R
inst/unitTests/NcdfReader_test.R
inst/unitTests/ScanAnnotationDataFrame_test.R
inst/unitTests/ScanAnnotationSQLite_test.R
inst/unitTests/SnpAnnotationDataFrame_test.R
inst/unitTests/SnpAnnotationSQLite_test.R
inst/unitTests/alleleFrequency_test.R
inst/unitTests/allequal_test.R
inst/unitTests/anomDetectBAF_test.R
inst/unitTests/apartSnpSelection_test.R
inst/unitTests/assocCoxPH_test.R
inst/unitTests/assocRegression_test.R
inst/unitTests/batchChisqTest_test.R
inst/unitTests/batchFisherTest_test.R
inst/unitTests/checkGenotypeFile_test.R
inst/unitTests/checkImputedDosageFile_test.R
inst/unitTests/checkIntensityFile_test.R
inst/unitTests/chromIntensityPlot_test.R
inst/unitTests/convertNcdfGds_test.R
inst/unitTests/createAffyIntensityFile_test.R
inst/unitTests/createDataFile_test.R
inst/unitTests/dupDosageCorAcrossDatasets_test.R
inst/unitTests/duplicateDiscordanceAcrossDatasets_test.R
inst/unitTests/duplicateDiscordance_test.R
inst/unitTests/exactHWE_test.R
inst/unitTests/findBAFvariance_test.R
inst/unitTests/gdsSubsetCheck_test.R
inst/unitTests/gdsSubset_test.R
inst/unitTests/genotypeToCharacter_test.R
inst/unitTests/getobj_test.R
inst/unitTests/hetByScanChrom_test.R
inst/unitTests/hetBySnpSex_test.R
inst/unitTests/ibdPlot_test.R
inst/unitTests/imputedDosageFile_test.R
inst/unitTests/meanIntensityByScanChrom_test.R
inst/unitTests/missingGenotypeByScanChrom_test.R
inst/unitTests/missingGenotypeBySnpSex_test.R
inst/unitTests/pedigreeCheck_test.R
inst/unitTests/pedigreeMaxUnrelated_test.R
inst/unitTests/pedigreePairwiseRelatedness_test.R
inst/unitTests/plinkUtils_test.R
inst/unitTests/pseudoautoIntensityPlot_test.R
inst/unitTests/qualityScoreByScan_test.R
inst/unitTests/qualityScoreBySnp_test.R
inst/unitTests/saveas_test.R
inst/unitTests/setMissingGenotypes_test.R
inst/unitTests/snpStats_test.R
inst/unitTests/vcfWrite_test.R
man
man/BAFfromClusterMeans.Rd
man/BAFfromGenotypes.Rd
man/GWASTools-package.Rd
man/GdsGenotypeReader-class.Rd
man/GdsIntensityReader-class.Rd
man/GdsReader-class.Rd
man/GenotypeData-class.Rd
man/HLA.Rd
man/IntensityData-class.Rd
man/MatrixGenotypeReader-class.Rd
man/NcdfGenotypeReader-class.Rd
man/NcdfIntensityReader-class.Rd
man/NcdfReader-class.Rd
man/ScanAnnotationDataFrame-class.Rd
man/ScanAnnotationSQLite-class.Rd
man/SnpAnnotationDataFrame-class.Rd
man/SnpAnnotationSQLite-class.Rd
man/alleleFrequency.Rd
man/allequal.Rd
man/anomDetectBAF.Rd
man/anomDetectLOH.Rd
man/anomIdentifyLowQuality.Rd
man/anomSegStats.Rd
man/apartSnpSelection.Rd
man/assocCoxPH.Rd
man/assocRegression.Rd
man/batchTest.Rd
man/centromeres.Rd
man/chromIntensityPlot.Rd
man/convertNcdfGds.Rd
man/createDataFile.Rd
man/defunct.Rd
man/duplicateDiscordance.Rd
man/duplicateDiscordanceAcrossDatasets.Rd
man/duplicateDiscordanceProbability.Rd
man/exactHWE.Rd
man/findBAFvariance.Rd
man/gdsSubset.Rd
man/genoClusterPlot.Rd
man/genotypeToCharacter.Rd
man/getVariable.Rd
man/getobj.Rd
man/hetByScanChrom.Rd
man/hetBySnpSex.Rd
man/ibdPlot.Rd
man/imputedDosageFile.Rd
man/intensityOutliersPlot.Rd
man/manhattanPlot.Rd
man/meanIntensityByScanChrom.Rd
man/mendelErr.Rd
man/mendelList.Rd
man/missingGenotypeByScanChrom.Rd
man/missingGenotypeBySnpSex.Rd
man/pasteSorted.Rd
man/pcaSnpFilters.Rd
man/pedigreeCheck.Rd
man/pedigreeDeleteDuplicates.Rd
man/pedigreeMaxUnrelated.Rd
man/pedigreePairwiseRelatedness.Rd
man/plinkUtils.Rd
man/pseudoautoIntensityPlot.Rd
man/pseudoautosomal.Rd
man/qqPlot.Rd
man/qualityScoreByScan.Rd
man/qualityScoreBySnp.Rd
man/readWriteFirst.Rd
man/relationsMeanVar.Rd
man/saveas.Rd
man/setMissingGenotypes.Rd
man/simulateGenotypeMatrix.Rd
man/snpCorrelationPlot.Rd
man/snpStats.Rd
man/vcfWrite.Rd
tests
tests/test.R
vignettes
vignettes/Affymetrix.Rnw
vignettes/DataCleaning.Rnw
vignettes/Formats.Rnw
GWASTools documentation built on May 20, 2017, 10:33 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

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