Package: GWASTools 1.53.0
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:
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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-1.53.0(bioc 3.21)GWASTools-1.52.0(bioc 3.20)
snpgeneticvariabilityqualitycontrolmicroarray
Last updated 23 days agofrom:804422bdd1. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 19 2024 |
| R-4.5-win | NOTE | Nov 19 2024 |
| R-4.5-linux | NOTE | Nov 19 2024 |
| R-4.4-win | NOTE | Nov 19 2024 |
| R-4.4-mac | NOTE | Nov 19 2024 |
| R-4.3-win | NOTE | Nov 19 2024 |
| R-4.3-mac | NOTE | Nov 19 2024 |
Exports:alleleFrequencyallequalanomDetectBAFanomDetectLOHanomFilterBAFanomIdentifyLowQualityanomSegmentBAFanomSegStatsanomStatsPlotapartSnpSelectionasSnpMatrixassocCoxPHassocRegressionautosomeCodeBAFfromClusterMeansBAFfromGenotypesbatchChisqTestbatchFisherTestcheckGenotypeFilecheckImputedDosageFilecheckIntensityFilecheckNcdfGdschromIntensityPlotcloseconvertGdsNcdfconvertNcdfGdscreateAffyIntensityFilecreateDataFilecurrentFilterdupDosageCorAcrossDatasetsduplicateDiscordanceduplicateDiscordanceAcrossDatasetsduplicateDiscordanceProbabilityexactHWEfindBAFvarianceGdsGenotypeReaderGdsIntensityReaderGdsReadergdsSubsetgdsSubsetCheckgenoClusterPlotgenoClusterPlotByBatchgenoDataAsVCFGenotypeBlockIteratorGenotypeDataGenotypeIteratorgenotypeToCharactergetAlleleAgetAlleleBgetAnnotationgetAttributegetBAlleleFreqgetChromosomegetDimensiongetDimensionNamesgetGenotypegetGenotypeSelectiongetLogRRatiogetMetadatagetNodeDescriptiongetobjgetPositiongetQualitygetQuerygetScanAnnotationgetScanIDgetScanVariablegetScanVariableNamesgetSexgetSnpAnnotationgetSnpIDgetSnpVariablegetSnpVariableNamesgetVariablegetVariableNamesgetXgetYhasBAlleleFreqhasCoordVariablehasLogRRatiohasQualityhasScanAnnotationhasScanVariablehasSexhasSnpAnnotationhasSnpVariablehasVariablehasXhasYhetByScanChromhetBySnpSexibdAreasDrawibdAssignRelatednessibdAssignRelatednessKingibdPlotimputedDosageFileIntensityDataintensityOutliersPlotiterateFilterkingIBS0FSCIlastFilterlastFilter<-manhattanPlotMatrixGenotypeReaderMchromCodemeanIntensityByScanChrommeanSdByChromWindowmedianSdOverAutosomesmendelErrmendelListmendelListAsDataFrameminorAlleleDetectionAccuracymissingGenotypeByScanChrommissingGenotypeBySnpSexNcdfGenotypeReaderNcdfIntensityReaderNcdfReadernscannsnpopenpasteSortedpedigreeCheckpedigreeDeleteDuplicatespedigreeMaxUnrelatedpedigreePairwiseRelatednessplinkCheckplinkWritepseudoautoIntensityPlotqqPlotqualityScoreByScanqualityScoreBySnpreadWriteFirstresetIteratorsaveasScanAnnotationDataFrameScanAnnotationSQLitesdByScanChromWindowsetMissingGenotypesshowsimulateGenotypeMatrixsimulateIntensityMatrixSnpAnnotationDataFrameSnpAnnotationSQLitesnpCorrelationPlotsnpFiltervcfCheckvcfWritewriteAnnotationwriteMetadataXchromCodeXYchromCodeYchromCode
Dependencies:backportsBiobaseBiocGenericsbitbit64blobbootbroomcachemclicliprcodetoolscpp11crayondata.tableDBIDNAcopydplyrfansifastmapforcatsforeachformula.toolsgdsfmtgenericsglmnetglueGWASExactHWhavenhmsiteratorsjomolatticelifecyclelme4lmtestlogistfmagrittrMASSMatrixMatrixModelsmemoisemgcvmiceminqamitmlnlmenloptrnnetnumDerivoperator.toolsordinalpanpillarpkgconfigplogrprettyunitsprogresspurrrquantregquantsmoothR6RcppRcppEigenreadrrlangrpartRSQLitesandwichshapeSparseMstringistringrsurvivaltibbletidyrtidyselecttzdbucminfutf8vctrsvroomwithrzoo
Data formats in GWASTools
Rendered fromFormats.Rnwusingutils::Sweaveon Nov 19 2024.Last update: 2018-09-26
Started: 2013-10-21
GWAS Data Cleaning
Rendered fromDataCleaning.Rnwusingutils::Sweaveon Nov 19 2024.Last update: 2018-09-26
Started: 2013-10-21
Preparing Affymetrix Data
Rendered fromAffymetrix.Rmdusingknitr::rmarkdownon Nov 19 2024.Last update: 2023-06-22
Started: 2023-06-22
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 |
