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

Files in this package

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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