Package: GWASTools 1.51.0

Stephanie M. Gogarten

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.

Authors:Stephanie M. Gogarten [aut], Cathy Laurie [aut], Tushar Bhangale [aut], Matthew P. Conomos [aut], Cecelia Laurie [aut], Michael Lawrence [aut], Caitlin McHugh [aut], Ian Painter [aut], Xiuwen Zheng [aut], Jess Shen [aut], Rohit Swarnkar [aut], Adrienne Stilp [aut], Sarah Nelson [aut], David Levine [aut], Sonali Kumari [ctb], Stephanie M. Gogarten [cre]

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GWASTools.pdf |GWASTools.html✨
GWASTools/json (API)
NEWS

# Install 'GWASTools' in R:

install.packages('GWASTools', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/smgogarten/gwastools/issues

Datasets:

HLA.hg18 - HLA region base positions
HLA.hg19 - HLA region base positions
HLA.hg38 - HLA region base positions
centromeres.hg18 - Centromere base positions
centromeres.hg19 - Centromere base positions
centromeres.hg38 - Centromere base positions
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
pcaSnpFilters.hg38 - Regions of SNP-PC correlation to filter for Principal Component Analysis
pseudoautosomal.hg18 - Pseudoautosomal region base positions
pseudoautosomal.hg19 - Pseudoautosomal region base positions
pseudoautosomal.hg38 - Pseudoautosomal region base positions
relationsMeanVar - Mean and Variance information for full-sibs, half-sibs, first-cousins

On BioConductor:GWASTools-1.51.0(bioc 3.20)GWASTools-1.50.0(bioc 3.19)

bioconductor-package

152 exports 3.58 score 84 dependencies 5 dependents 17 mentions

Last updated 2 months agofrom:cfd60b4514

Exports:alleleFrequency allequal anomDetectBAF anomDetectLOH anomFilterBAF anomIdentifyLowQuality anomSegmentBAF anomSegStats anomStatsPlot apartSnpSelection asSnpMatrix assocCoxPH assocRegression autosomeCode BAFfromClusterMeans BAFfromGenotypes batchChisqTest batchFisherTest checkGenotypeFile checkImputedDosageFile checkIntensityFile checkNcdfGds chromIntensityPlot close convertGdsNcdf convertNcdfGds createAffyIntensityFile createDataFile currentFilter dupDosageCorAcrossDatasets duplicateDiscordance duplicateDiscordanceAcrossDatasets duplicateDiscordanceProbability exactHWE findBAFvariance GdsGenotypeReader GdsIntensityReader GdsReader gdsSubset gdsSubsetCheck genoClusterPlot genoClusterPlotByBatch genoDataAsVCF GenotypeBlockIterator GenotypeData GenotypeIterator genotypeToCharacter getAlleleA getAlleleB getAnnotation getAttribute getBAlleleFreq getChromosome getDimension getDimensionNames getGenotype getGenotypeSelection getLogRRatio getMetadata getNodeDescription getobj getPosition getQuality getQuery getScanAnnotation getScanID getScanVariable getScanVariableNames getSex getSnpAnnotation getSnpID getSnpVariable getSnpVariableNames getVariable getVariableNames getX getY hasBAlleleFreq hasCoordVariable hasLogRRatio hasQuality hasScanAnnotation hasScanVariable hasSex hasSnpAnnotation hasSnpVariable hasVariable hasX hasY hetByScanChrom hetBySnpSex ibdAreasDraw ibdAssignRelatedness ibdAssignRelatednessKing ibdPlot imputedDosageFile IntensityData intensityOutliersPlot iterateFilter kingIBS0FSCI lastFilter lastFilter<-manhattanPlot MatrixGenotypeReader MchromCode meanIntensityByScanChrom meanSdByChromWindow medianSdOverAutosomes mendelErr mendelList mendelListAsDataFrame minorAlleleDetectionAccuracy missingGenotypeByScanChrom missingGenotypeBySnpSex NcdfGenotypeReader NcdfIntensityReader NcdfReader nscan nsnp open pasteSorted pedigreeCheck pedigreeDeleteDuplicates pedigreeMaxUnrelated pedigreePairwiseRelatedness plinkCheck plinkWrite pseudoautoIntensityPlot qqPlot qualityScoreByScan qualityScoreBySnp readWriteFirst resetIterator saveas ScanAnnotationDataFrame ScanAnnotationSQLite sdByScanChromWindow setMissingGenotypes show simulateGenotypeMatrix simulateIntensityMatrix SnpAnnotationDataFrame SnpAnnotationSQLite snpCorrelationPlot snpFilter vcfCheck vcfWrite writeAnnotation writeMetadata XchromCode XYchromCode YchromCode

Dependencies:backports Biobase BiocGenerics bit bit64 blob boot broom cachem cli clipr codetools cpp11 crayon data.table DBI DNAcopy dplyr fansi fastmap forcats foreach formula.tools gdsfmt generics glmnet glue GWASExactHW haven hms iterators jomo lattice lifecycle lme4 lmtest logistf magrittr MASS Matrix MatrixModels memoise mgcv mice minqa mitml nlme nloptr nnet numDeriv operator.tools ordinal pan pillar pkgconfig plogr prettyunits progress purrr quantreg quantsmooth R6 Rcpp RcppEigen readr rlang rpart RSQLite sandwich shape SparseM stringi stringr survival tibble tidyr tidyselect tzdb ucminf utf8 vctrs vroom withr zoo

Data formats in GWASTools

Rendered fromFormats.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2018-09-26
Started: 2013-10-21

GWAS Data Cleaning

Rendered fromDataCleaning.Rnwusingutils::Sweaveon Jul 03 2024.

Last update: 2018-09-26
Started: 2013-10-21

Preparing Affymetrix Data

GENEVA Coordinating Center, Sonali Kumari

Rendered fromAffymetrix.Rmdusingknitr::rmarkdownon Jul 03 2024.

Last update: 2023-06-22
Started: 2023-06-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Tools for Genome Wide Association Studies	GWASTools-package GWASTools
Allelic frequency	alleleFrequency
Test if two objects have the same elements	allequal
BAF Method for Chromosome Anomaly Detection	anomDetectBAF anomFilterBAF anomSegmentBAF
LOH Method for Chromosome Anomaly Detection	anomDetectLOH
Identify low quality samples	anomIdentifyLowQuality
Calculate LRR and BAF statistics for anomalous segments	anomSegStats anomStatsPlot
Random selection of SNPs	apartSnpSelection
Utilities for snpStats	asSnpMatrix
Cox proportional hazards	assocCoxPH
Association testing with regression	assocRegression
B Allele Frequency & Log R Ratio Calculation	BAFfromClusterMeans
B Allele Frequency & Log R Ratio Calculation	BAFfromGenotypes
Batch Effects of Genotyping	batchChisqTest batchFisherTest
Centromere base positions	centromeres centromeres.hg18 centromeres.hg19 centromeres.hg38
Plot B Allele Frequency and/or Log R Ratio, R or Theta values for samples by probe position on a chromosome	chromIntensityPlot
Convert between NetCDF and GDS format	checkNcdfGds convertGdsNcdf convertNcdfGds
Write genotypic calls and/or associated metrics to a GDS or netCDF file.	checkGenotypeFile checkIntensityFile createAffyIntensityFile createDataFile
Duplicate discordance	duplicateDiscordance
Functions to check discordance and allelic dosage correlation across datasets	dupDosageCorAcrossDatasets duplicateDiscordanceAcrossDatasets minorAlleleDetectionAccuracy
Probability of duplicate discordance	duplicateDiscordanceProbability
Hardy-Weinberg Equilibrium testing	exactHWE
Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation	findBAFvariance meanSdByChromWindow medianSdOverAutosomes sdByScanChromWindow
Class GdsGenotypeReader	autosomeCode,GdsGenotypeReader-method GdsGenotypeReader GdsGenotypeReader-class getAlleleA,GdsGenotypeReader-method getAlleleB,GdsGenotypeReader-method getChromosome,GdsGenotypeReader-method getGenotype,GdsGenotypeReader-method getGenotypeSelection,GdsGenotypeReader-method getPosition,GdsGenotypeReader-method getScanID,GdsGenotypeReader-method getSnpID,GdsGenotypeReader-method getVariable,GdsGenotypeReader-method MchromCode,GdsGenotypeReader-method nscan,GdsGenotypeReader-method nsnp,GdsGenotypeReader-method XchromCode,GdsGenotypeReader-method XYchromCode,GdsGenotypeReader-method YchromCode,GdsGenotypeReader-method
Class GdsIntensityReader	autosomeCode,GdsIntensityReader-method GdsIntensityReader GdsIntensityReader-class getBAlleleFreq,GdsIntensityReader-method getChromosome,GdsIntensityReader-method getLogRRatio,GdsIntensityReader-method getPosition,GdsIntensityReader-method getQuality,GdsIntensityReader-method getScanID,GdsIntensityReader-method getSnpID,GdsIntensityReader-method getVariable,GdsIntensityReader-method getX,GdsIntensityReader-method getY,GdsIntensityReader-method hasBAlleleFreq,GdsIntensityReader-method hasLogRRatio,GdsIntensityReader-method hasQuality,GdsIntensityReader-method hasX,GdsIntensityReader-method hasY,GdsIntensityReader-method MchromCode,GdsIntensityReader-method nscan,GdsIntensityReader-method nsnp,GdsIntensityReader-method XchromCode,GdsIntensityReader-method XYchromCode,GdsIntensityReader-method YchromCode,GdsIntensityReader-method
Class GdsReader	close,GdsReader-method GdsReader GdsReader-class getAttribute,GdsReader-method getDimension,GdsReader-method getNodeDescription,GdsReader-method getVariable,GdsReader-method getVariableNames,GdsReader-method hasVariable,GdsReader-method open,GdsReader-method show,GdsReader-method
Write a subset of data in a GDS file to a new GDS file	gdsSubset gdsSubsetCheck
SNP cluster plots	genoClusterPlot genoClusterPlotByBatch
Class GenotypeData	autosomeCode,GenotypeData-method close,GenotypeData-method GenotypeData GenotypeData-class getAlleleA,GenotypeData-method getAlleleB,GenotypeData-method getChromosome,GenotypeData-method getGenotype,GenotypeData-method getGenotypeSelection,GenotypeData-method getPosition,GenotypeData-method getScanAnnotation,GenotypeData-method getScanID,GenotypeData-method getScanVariable,GenotypeData-method getScanVariableNames,GenotypeData-method getSex,GenotypeData-method getSnpAnnotation,GenotypeData-method getSnpID,GenotypeData-method getSnpVariable,GenotypeData-method getSnpVariableNames,GenotypeData-method getVariable,GenotypeData-method hasScanAnnotation,GenotypeData-method hasScanVariable,GenotypeData-method hasSex,GenotypeData-method hasSnpAnnotation,GenotypeData-method hasSnpVariable,GenotypeData-method hasVariable,GenotypeData-method MchromCode,GenotypeData-method nscan,GenotypeData-method nsnp,GenotypeData-method open,GenotypeData-method show,GenotypeData-method XchromCode,GenotypeData-method XYchromCode,GenotypeData-method YchromCode,GenotypeData-method
Class GenotypeIterator	currentFilter currentFilter,GenotypeIterator-method GenotypeBlockIterator GenotypeBlockIterator-class GenotypeIterator GenotypeIterator-class getAlleleA,GenotypeIterator-method getAlleleB,GenotypeIterator-method getChromosome,GenotypeIterator-method getGenotypeSelection,GenotypeIterator-method getPosition,GenotypeIterator-method getSnpID,GenotypeIterator-method getSnpVariable,GenotypeIterator-method iterateFilter iterateFilter,GenotypeIterator-method lastFilter lastFilter,GenotypeIterator-method lastFilter<- lastFilter<-,GenotypeIterator,numeric-method resetIterator resetIterator,GenotypeIterator-method snpFilter snpFilter,GenotypeIterator-method
Convert number of A alleles to character genotypes	genotypeToCharacter
Get an R object stored in an Rdata file	getobj
Accessors for variables in GenotypeData and IntensityData classes and their component classes	autosomeCode getAlleleA getAlleleB getAnnotation getAttribute getBAlleleFreq getChromosome getDimension getGenotype getGenotypeSelection getLogRRatio getMetadata getNodeDescription getPosition getQuality getQuery getScanAnnotation getScanID getScanVariable getScanVariableNames getSex getSnpAnnotation getSnpID getSnpVariable getSnpVariableNames getVariable getVariableNames getX getY hasBAlleleFreq hasLogRRatio hasQuality hasScanAnnotation hasScanVariable hasSex hasSnpAnnotation hasSnpVariable hasVariable hasX hasY MchromCode nscan nsnp writeAnnotation writeMetadata XchromCode XYchromCode YchromCode
Defunct Functions in Package 'GWASTools'	assocTestCPH assocTestFisherExact assocTestRegression convertVcfGds gdsCheckImputedDosage gdsImputedDosage gdsSetMissingGenotypes gwasExactHW GWASTools-defunct ncdfAddData ncdfAddIntensity ncdfCheckGenotype ncdfCheckIntensity ncdfCreate ncdfImputedDosage ncdfSetMissingGenotypes ncdfSubset ncdfSubsetCheck plinkToNcdf
Heterozygosity rates by scan and chromosome	hetByScanChrom
Heterozygosity by SNP and sex	hetBySnpSex
HLA region base positions	HLA HLA.hg18 HLA.hg19 HLA.hg38
Plot theoretical and observed identity by descent values and assign relationships	ibdAreasDraw ibdAssignRelatedness ibdAssignRelatednessKing ibdPlot kingIBS0FSCI
Create and check a GDS or NetCDF file with imputed dosages	checkImputedDosageFile imputedDosageFile
Class IntensityData	autosomeCode,IntensityData-method close,IntensityData-method getBAlleleFreq,IntensityData-method getChromosome,IntensityData-method getLogRRatio,IntensityData-method getPosition,IntensityData-method getQuality,IntensityData-method getScanID,IntensityData-method getScanVariable,IntensityData-method getScanVariableNames,IntensityData-method getSex,IntensityData-method getSnpID,IntensityData-method getSnpVariable,IntensityData-method getSnpVariableNames,IntensityData-method getVariable,IntensityData-method getX,IntensityData-method getY,IntensityData-method hasBAlleleFreq,IntensityData-method hasLogRRatio,IntensityData-method hasQuality,IntensityData-method hasScanAnnotation,IntensityData-method hasScanVariable,IntensityData-method hasSex,IntensityData-method hasSnpAnnotation,IntensityData-method hasSnpVariable,IntensityData-method hasVariable,IntensityData-method hasX,IntensityData-method hasY,IntensityData-method IntensityData IntensityData-class MchromCode,IntensityData-method nscan,IntensityData-method nsnp,IntensityData-method open,IntensityData-method show,IntensityData-method XchromCode,IntensityData-method XYchromCode,IntensityData-method YchromCode,IntensityData-method
Plot mean intensity and highlight outliers	intensityOutliersPlot
Manhattan plot for genome wide association tests	manhattanPlot
Class MatrixGenotypeReader	autosomeCode,MatrixGenotypeReader-method getChromosome,MatrixGenotypeReader-method getGenotype,MatrixGenotypeReader-method getGenotypeSelection,MatrixGenotypeReader-method getPosition,MatrixGenotypeReader-method getScanID,MatrixGenotypeReader-method getSnpID,MatrixGenotypeReader-method MatrixGenotypeReader MatrixGenotypeReader-class MchromCode,MatrixGenotypeReader-method nscan,MatrixGenotypeReader-method nsnp,MatrixGenotypeReader-method show,MatrixGenotypeReader-method XchromCode,MatrixGenotypeReader-method XYchromCode,MatrixGenotypeReader-method YchromCode,MatrixGenotypeReader-method
Calculate Means and Standard Deviations of Intensities	meanIntensityByScanChrom
Mendelian Error Checking	mendelErr
Mendelian Error Checking	mendelList mendelListAsDataFrame
Missing Counts per Scan per Chromosome	missingGenotypeByScanChrom
Missing Counts per SNP by Sex	missingGenotypeBySnpSex
Class NcdfGenotypeReader	autosomeCode,NcdfGenotypeReader-method getChromosome,NcdfGenotypeReader-method getGenotype,NcdfGenotypeReader-method getPosition,NcdfGenotypeReader-method getScanID,NcdfGenotypeReader-method getSnpID,NcdfGenotypeReader-method getVariable,NcdfGenotypeReader-method MchromCode,NcdfGenotypeReader-method NcdfGenotypeReader NcdfGenotypeReader-class nscan,NcdfGenotypeReader-method nsnp,NcdfGenotypeReader-method XchromCode,NcdfGenotypeReader-method XYchromCode,NcdfGenotypeReader-method YchromCode,NcdfGenotypeReader-method
Class NcdfIntensityReader	autosomeCode,NcdfIntensityReader-method getBAlleleFreq,NcdfIntensityReader-method getChromosome,NcdfIntensityReader-method getLogRRatio,NcdfIntensityReader-method getPosition,NcdfIntensityReader-method getQuality,NcdfIntensityReader-method getScanID,NcdfIntensityReader-method getSnpID,NcdfIntensityReader-method getVariable,NcdfIntensityReader-method getX,NcdfIntensityReader-method getY,NcdfIntensityReader-method hasBAlleleFreq,NcdfIntensityReader-method hasLogRRatio,NcdfIntensityReader-method hasQuality,NcdfIntensityReader-method hasX,NcdfIntensityReader-method hasY,NcdfIntensityReader-method MchromCode,NcdfIntensityReader-method NcdfIntensityReader NcdfIntensityReader-class nscan,NcdfIntensityReader-method nsnp,NcdfIntensityReader-method XchromCode,NcdfIntensityReader-method XYchromCode,NcdfIntensityReader-method YchromCode,NcdfIntensityReader-method
Class NcdfReader	close,NcdfReader-method getAttribute,NcdfReader-method getDimension,NcdfReader-method getDimensionNames getDimensionNames,NcdfReader-method getVariable,NcdfReader-method getVariableNames,NcdfReader-method hasCoordVariable hasCoordVariable,NcdfReader-method hasVariable,NcdfReader-method NcdfReader NcdfReader-class open,NcdfReader-method show,NcdfReader-method
Paste two vectors sorted pairwise	pasteSorted
Regions of SNP-PC correlation to filter for Principal Component Analysis	pcaSnpFilters pcaSnpFilters.hg18 pcaSnpFilters.hg19 pcaSnpFilters.hg38
Testing for internal consistency of pedigrees	pedigreeCheck
Remove duplicates from a pedigree	pedigreeDeleteDuplicates
Find a maximal set of unrelated individuals in a subset of a pedigree.	pedigreeMaxUnrelated
Assign relatedness from pedigree data	pedigreePairwiseRelatedness
Utilities to create and check PLINK files	plinkCheck plinkWrite
Plot B Allele Frequency and Log R Ratio for the X and Y chromosomes, overlaying XY SNPs	pseudoautoIntensityPlot
Pseudoautosomal region base positions	pseudoautosomal pseudoautosomal.hg18 pseudoautosomal.hg19 pseudoautosomal.hg38
QQ plot for genome wide assocation studies	qqPlot
Mean and median quality score for scans	qualityScoreByScan
Mean and median quality score for SNPs	qualityScoreBySnp
Read and write the first n lines of a file	readWriteFirst
Mean and Variance information for full-sibs, half-sibs, first-cousins	relationsMeanVar
Save an R object with a new name	saveas
Class ScanAnotationDataFrame	getAnnotation,ScanAnnotationDataFrame-method getMetadata,ScanAnnotationDataFrame-method getScanID,ScanAnnotationDataFrame-method getSex,ScanAnnotationDataFrame-method getVariable,ScanAnnotationDataFrame-method getVariableNames,ScanAnnotationDataFrame-method hasSex,ScanAnnotationDataFrame-method hasVariable,ScanAnnotationDataFrame-method ScanAnnotationDataFrame ScanAnnotationDataFrame-class
Class ScanAnotationSQLite	close,ScanAnnotationSQLite-method getAnnotation,ScanAnnotationSQLite-method getMetadata,ScanAnnotationSQLite-method getQuery,ScanAnnotationSQLite-method getScanID,ScanAnnotationSQLite-method getSex,ScanAnnotationSQLite-method getVariable,ScanAnnotationSQLite-method getVariableNames,ScanAnnotationSQLite-method hasSex,ScanAnnotationSQLite-method hasVariable,ScanAnnotationSQLite-method nscan,ScanAnnotationSQLite-method open,ScanAnnotationSQLite-method ScanAnnotationSQLite ScanAnnotationSQLite-class show,ScanAnnotationSQLite-method writeAnnotation,ScanAnnotationSQLite-method writeMetadata,ScanAnnotationSQLite-method
Write a new netCDF or GDS file, setting certain SNPs to missing	setMissingGenotypes
Simulate Genotype or Intensity Matrix & Load into GDS/NetCDF File	simulateGenotypeMatrix simulateIntensityMatrix
Class SnpAnotationDataFrame	autosomeCode,SnpAnnotationDataFrame-method getAlleleA,SnpAnnotationDataFrame-method getAlleleB,SnpAnnotationDataFrame-method getAnnotation,SnpAnnotationDataFrame-method getChromosome,SnpAnnotationDataFrame-method getMetadata,SnpAnnotationDataFrame-method getPosition,SnpAnnotationDataFrame-method getSnpID,SnpAnnotationDataFrame-method getVariable,SnpAnnotationDataFrame-method getVariableNames,SnpAnnotationDataFrame-method hasVariable,SnpAnnotationDataFrame-method MchromCode,SnpAnnotationDataFrame-method SnpAnnotationDataFrame SnpAnnotationDataFrame-class XchromCode,SnpAnnotationDataFrame-method XYchromCode,SnpAnnotationDataFrame-method YchromCode,SnpAnnotationDataFrame-method
Class SnpAnotationSQLite	autosomeCode,SnpAnnotationSQLite-method close,SnpAnnotationSQLite-method getAlleleA,SnpAnnotationSQLite-method getAlleleB,SnpAnnotationSQLite-method getAnnotation,SnpAnnotationSQLite-method getChromosome,SnpAnnotationSQLite-method getMetadata,SnpAnnotationSQLite-method getPosition,SnpAnnotationSQLite-method getQuery,SnpAnnotationSQLite-method getSnpID,SnpAnnotationSQLite-method getVariable,SnpAnnotationSQLite-method getVariableNames,SnpAnnotationSQLite-method hasVariable,SnpAnnotationSQLite-method MchromCode,SnpAnnotationSQLite-method nsnp,SnpAnnotationSQLite-method open,SnpAnnotationSQLite-method show,SnpAnnotationSQLite-method SnpAnnotationSQLite SnpAnnotationSQLite-class writeAnnotation,SnpAnnotationSQLite-method writeMetadata,SnpAnnotationSQLite-method XchromCode,SnpAnnotationSQLite-method XYchromCode,SnpAnnotationSQLite-method YchromCode,SnpAnnotationSQLite-method
SNP correlation plot	snpCorrelationPlot
Utility to write VCF file	genoDataAsVCF vcfCheck vcfWrite