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.

Author
Stephanie 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 publication
None
Maintainer
Stephanie M. Gogarten <sdmorris@u.washington.edu>, Adrienne Stilp <amstilp@u.washington.edu>
License
Artistic-2.0
Version
1.20.0

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