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"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" ] }, { "page": "GenotypeIterator-class", "title": "Class GenotypeIterator", "topics": [ "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" ] }, { "page": "genotypeToCharacter", "title": "Convert number of A alleles to character genotypes", "topics": [ "genotypeToCharacter" ] }, { "page": "getobj", "title": "Get an R object stored in an Rdata file", "topics": [ "getobj" ] }, { "page": "getVariable", "title": "Accessors for variables in GenotypeData and IntensityData classes and their component classes", "topics": [ "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" ] }, { "page": "defunct", "title": "Defunct Functions in Package 'GWASTools'", "topics": [ "assocTestCPH", "assocTestFisherExact", "assocTestRegression", "convertVcfGds", "gdsCheckImputedDosage", "gdsImputedDosage", "gdsSetMissingGenotypes", "gwasExactHW", "GWASTools-defunct", "ncdfAddData", "ncdfAddIntensity", "ncdfCheckGenotype", "ncdfCheckIntensity", "ncdfCreate", "ncdfImputedDosage", "ncdfSetMissingGenotypes", "ncdfSubset", "ncdfSubsetCheck", "plinkToNcdf" ] }, { "page": "hetByScanChrom", "title": "Heterozygosity rates by scan and chromosome", "topics": [ "hetByScanChrom" ] }, { "page": "hetBySnpSex", "title": "Heterozygosity by SNP and sex", "topics": [ "hetBySnpSex" ] }, { "page": "HLA", "title": "HLA region base positions", "topics": [ "HLA", "HLA.hg18", "HLA.hg19", "HLA.hg38" ] }, { "page": "ibdPlot", "title": "Plot theoretical and observed identity by descent values and assign relationships", "topics": [ "ibdAreasDraw", "ibdAssignRelatedness", "ibdAssignRelatednessKing", "ibdPlot", "kingIBS0FSCI" ] }, { "page": "imputedDosageFile", "title": "Create and check a GDS or NetCDF file with imputed dosages", "topics": [ "checkImputedDosageFile", "imputedDosageFile" ] }, { "page": "IntensityData-class", "title": "Class IntensityData", "topics": [ "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" ] }, { "page": "intensityOutliersPlot", "title": "Plot mean intensity and highlight outliers", "topics": [ "intensityOutliersPlot" ] }, { "page": "manhattanPlot", "title": "Manhattan plot for genome wide association tests", "topics": [ "manhattanPlot" ] }, { "page": "MatrixGenotypeReader-class", "title": "Class MatrixGenotypeReader", "topics": [ "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" ] }, { "page": "meanIntensityByScanChrom", "title": "Calculate Means and Standard Deviations of Intensities", "topics": [ "meanIntensityByScanChrom" ] }, { "page": "mendelErr", "title": "Mendelian Error Checking", "topics": [ "mendelErr" ] }, { "page": "mendelList", "title": "Mendelian Error Checking", "topics": [ "mendelList", "mendelListAsDataFrame" ] }, { "page": "missingGenotypeByScanChrom", "title": "Missing Counts per Scan per Chromosome", "topics": [ "missingGenotypeByScanChrom" ] }, { "page": "missingGenotypeBySnpSex", "title": "Missing Counts per SNP by Sex", "topics": [ "missingGenotypeBySnpSex" ] }, { "page": "NcdfGenotypeReader-class", "title": "Class NcdfGenotypeReader", "topics": [ "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" ] }, { "page": "NcdfIntensityReader-class", "title": "Class NcdfIntensityReader", "topics": [ "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" ] }, { "page": "NcdfReader-class", "title": "Class NcdfReader", "topics": [ "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" ] }, { "page": "pasteSorted", "title": "Paste two vectors sorted pairwise", "topics": [ "pasteSorted" ] }, { "page": "pcaSnpFilters", "title": "Regions of SNP-PC correlation to filter for Principal Component Analysis", "topics": [ "pcaSnpFilters", "pcaSnpFilters.hg18", "pcaSnpFilters.hg19", "pcaSnpFilters.hg38" ] }, { "page": "pedigreeCheck", "title": "Testing for internal consistency of pedigrees", "topics": [ "pedigreeCheck" ] }, { "page": "pedigreeDeleteDuplicates", "title": "Remove duplicates from a pedigree", "topics": [ "pedigreeDeleteDuplicates" ] }, { "page": "pedigreeMaxUnrelated", "title": "Find a maximal set of unrelated individuals in a subset of a pedigree.", "topics": [ "pedigreeMaxUnrelated" ] }, { "page": "pedigreePairwiseRelatedness", "title": "Assign relatedness from pedigree data", "topics": [ "pedigreePairwiseRelatedness" ] }, { "page": "plinkUtils", "title": "Utilities to create and check PLINK files", "topics": [ "plinkCheck", "plinkWrite" ] }, { "page": "pseudoautoIntensityPlot", "title": "Plot B Allele Frequency and Log R Ratio for the X and Y chromosomes, overlaying XY SNPs", "topics": [ "pseudoautoIntensityPlot" ] }, { "page": "pseudoautosomal", "title": "Pseudoautosomal region base positions", "topics": [ "pseudoautosomal", "pseudoautosomal.hg18", "pseudoautosomal.hg19", "pseudoautosomal.hg38" ] }, { "page": "qqPlot", "title": "QQ plot for genome wide assocation studies", "topics": [ "qqPlot" ] }, { "page": "qualityScoreByScan", "title": "Mean and median quality score for scans", "topics": [ "qualityScoreByScan" ] }, { "page": "qualityScoreBySnp", "title": "Mean and median quality score for SNPs", "topics": [ "qualityScoreBySnp" ] }, { "page": "readWriteFirst", "title": "Read and write the first n lines of a file", "topics": [ "readWriteFirst" ] }, { "page": "relationsMeanVar", "title": "Mean and Variance information for full-sibs, half-sibs, first-cousins", "topics": [ "relationsMeanVar" ] }, { "page": "saveas", "title": "Save an R object with a new name", "topics": [ "saveas" ] }, { "page": "ScanAnnotationDataFrame-class", "title": "Class ScanAnotationDataFrame", "topics": [ "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" ] }, { "page": "ScanAnnotationSQLite-class", "title": "Class ScanAnotationSQLite", "topics": [ "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" ] }, { "page": "setMissingGenotypes", "title": "Write a new netCDF or GDS file, setting certain SNPs to missing", "topics": [ "setMissingGenotypes" ] }, { "page": "simulateGenotypeMatrix", "title": "Simulate Genotype or Intensity Matrix & Load into GDS/NetCDF File", "topics": [ "simulateGenotypeMatrix", "simulateIntensityMatrix" ] }, { "page": "SnpAnnotationDataFrame-class", "title": "Class SnpAnotationDataFrame", "topics": [ "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" ] }, { "page": "SnpAnnotationSQLite-class", "title": "Class SnpAnotationSQLite", "topics": [ "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" ] }, { "page": "snpCorrelationPlot", "title": "SNP correlation plot", "topics": [ "snpCorrelationPlot" ] }, { "page": "vcfWrite", "title": "Utility to write VCF file", "topics": [ "genoDataAsVCF", "vcfCheck", "vcfWrite" ] } ], "_readme": "https://github.com/bioc/GWASTools/raw/RELEASE_3_23/README.md", "_rundeps": [ "backports", "Biobase", "BiocGenerics", "bit", "bit64", "blob", "boot", "broom", "cachem", "cli", "clipr", "codetools", "cpp11", "crayon", "data.table", "DBI", "DNAcopy", "dplyr", "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", "prettyunits", "progress", "purrr", "quantreg", "quantsmooth", "R6", "rbibutils", "Rcpp", "RcppEigen", "Rdpack", "readr", "reformulas", 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