Tools for Genome Wide Association Studies
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Documentation for package ‘GWASTools’ version 1.54.0
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A B C D E F G H I K L M N O P Q R S V W X Y
| GWASTools-package | Tools for Genome Wide Association Studies |
-- A --
| 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 |
| anomFilterBAF | BAF Method for Chromosome Anomaly Detection |
| anomIdentifyLowQuality | Identify low quality samples |
| anomSegmentBAF | BAF Method for Chromosome Anomaly Detection |
| anomSegStats | Calculate LRR and BAF statistics for anomalous segments |
| anomStatsPlot | Calculate LRR and BAF statistics for anomalous segments |
| apartSnpSelection | Random selection of SNPs |
| asSnpMatrix | Utilities for snpStats |
| assocCoxPH | Cox proportional hazards |
| assocRegression | Association testing with regression |
| assocTestCPH | Defunct Functions in Package 'GWASTools' |
| assocTestFisherExact | Defunct Functions in Package 'GWASTools' |
| assocTestRegression | Defunct Functions in Package 'GWASTools' |
| autosomeCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| autosomeCode-method | Class GdsGenotypeReader |
| autosomeCode-method | Class GdsIntensityReader |
| autosomeCode-method | Class GenotypeData |
| autosomeCode-method | Class IntensityData |
| autosomeCode-method | Class MatrixGenotypeReader |
| autosomeCode-method | Class NcdfGenotypeReader |
| autosomeCode-method | Class NcdfIntensityReader |
| autosomeCode-method | Class SnpAnotationDataFrame |
| autosomeCode-method | Class SnpAnotationSQLite |
-- B --
| BAFfromClusterMeans | B Allele Frequency & Log R Ratio Calculation |
| BAFfromGenotypes | B Allele Frequency & Log R Ratio Calculation |
| batchChisqTest | Batch Effects of Genotyping |
| batchFisherTest | Batch Effects of Genotyping |
-- C --
| centromeres | Centromere base positions |
| centromeres.hg18 | Centromere base positions |
| centromeres.hg19 | Centromere base positions |
| centromeres.hg38 | Centromere base positions |
| checkGenotypeFile | Write genotypic calls and/or associated metrics to a GDS or netCDF file. |
| checkImputedDosageFile | Create and check a GDS or NetCDF file with imputed dosages |
| checkIntensityFile | Write genotypic calls and/or associated metrics to a GDS or netCDF file. |
| checkNcdfGds | Convert between NetCDF and GDS format |
| chromIntensityPlot | Plot B Allele Frequency and/or Log R Ratio, R or Theta values for samples by probe position on a chromosome |
| close-method | Class GdsReader |
| close-method | Class GenotypeData |
| close-method | Class IntensityData |
| close-method | Class NcdfReader |
| close-method | Class ScanAnotationSQLite |
| close-method | Class SnpAnotationSQLite |
| convertGdsNcdf | Convert between NetCDF and GDS format |
| convertNcdfGds | Convert between NetCDF and GDS format |
| convertVcfGds | Defunct Functions in Package 'GWASTools' |
| createAffyIntensityFile | Write genotypic calls and/or associated metrics to a GDS or netCDF file. |
| createDataFile | Write genotypic calls and/or associated metrics to a GDS or netCDF file. |
| currentFilter | Class GenotypeIterator |
| currentFilter-method | Class GenotypeIterator |
-- D --
| dupDosageCorAcrossDatasets | Functions to check discordance and allelic dosage correlation across datasets |
| duplicateDiscordance | Duplicate discordance |
| duplicateDiscordanceAcrossDatasets | Functions to check discordance and allelic dosage correlation across datasets |
| duplicateDiscordanceProbability | Probability of duplicate discordance |
-- E --
| exactHWE | Hardy-Weinberg Equilibrium testing |
-- F --
| findBAFvariance | Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation |
-- G --
| gdsCheckImputedDosage | Defunct Functions in Package 'GWASTools' |
| GdsGenotypeReader | Class GdsGenotypeReader |
| GdsGenotypeReader-class | Class GdsGenotypeReader |
| gdsImputedDosage | Defunct Functions in Package 'GWASTools' |
| GdsIntensityReader | Class GdsIntensityReader |
| GdsIntensityReader-class | Class GdsIntensityReader |
| GdsReader | Class GdsReader |
| GdsReader-class | Class GdsReader |
| gdsSetMissingGenotypes | Defunct Functions in Package 'GWASTools' |
| gdsSubset | Write a subset of data in a GDS file to a new GDS file |
| gdsSubsetCheck | Write a subset of data in a GDS file to a new GDS file |
| genoClusterPlot | SNP cluster plots |
| genoClusterPlotByBatch | SNP cluster plots |
| genoDataAsVCF | Utility to write VCF file |
| GenotypeBlockIterator | Class GenotypeIterator |
| GenotypeBlockIterator-class | Class GenotypeIterator |
| GenotypeData | Class GenotypeData |
| GenotypeData-class | Class GenotypeData |
| GenotypeIterator | Class GenotypeIterator |
| GenotypeIterator-class | Class GenotypeIterator |
| genotypeToCharacter | Convert number of A alleles to character genotypes |
| getAlleleA | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getAlleleA-method | Class GdsGenotypeReader |
| getAlleleA-method | Class GenotypeData |
| getAlleleA-method | Class GenotypeIterator |
| getAlleleA-method | Class SnpAnotationDataFrame |
| getAlleleA-method | Class SnpAnotationSQLite |
| getAlleleB | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getAlleleB-method | Class GdsGenotypeReader |
| getAlleleB-method | Class GenotypeData |
| getAlleleB-method | Class GenotypeIterator |
| getAlleleB-method | Class SnpAnotationDataFrame |
| getAlleleB-method | Class SnpAnotationSQLite |
| getAnnotation | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getAnnotation-method | Class ScanAnotationDataFrame |
| getAnnotation-method | Class ScanAnotationSQLite |
| getAnnotation-method | Class SnpAnotationDataFrame |
| getAnnotation-method | Class SnpAnotationSQLite |
| getAttribute | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getAttribute-method | Class GdsReader |
| getAttribute-method | Class NcdfReader |
| getBAlleleFreq | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getBAlleleFreq-method | Class GdsIntensityReader |
| getBAlleleFreq-method | Class IntensityData |
| getBAlleleFreq-method | Class NcdfIntensityReader |
| getChromosome | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getChromosome-method | Class GdsGenotypeReader |
| getChromosome-method | Class GdsIntensityReader |
| getChromosome-method | Class GenotypeData |
| getChromosome-method | Class GenotypeIterator |
| getChromosome-method | Class IntensityData |
| getChromosome-method | Class MatrixGenotypeReader |
| getChromosome-method | Class NcdfGenotypeReader |
| getChromosome-method | Class NcdfIntensityReader |
| getChromosome-method | Class SnpAnotationDataFrame |
| getChromosome-method | Class SnpAnotationSQLite |
| getDimension | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getDimension-method | Class GdsReader |
| getDimension-method | Class NcdfReader |
| getDimensionNames | Class NcdfReader |
| getDimensionNames-method | Class NcdfReader |
| getGenotype | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getGenotype-method | Class GdsGenotypeReader |
| getGenotype-method | Class GenotypeData |
| getGenotype-method | Class MatrixGenotypeReader |
| getGenotype-method | Class NcdfGenotypeReader |
| getGenotypeSelection | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getGenotypeSelection-method | Class GdsGenotypeReader |
| getGenotypeSelection-method | Class GenotypeData |
| getGenotypeSelection-method | Class GenotypeIterator |
| getGenotypeSelection-method | Class MatrixGenotypeReader |
| getLogRRatio | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getLogRRatio-method | Class GdsIntensityReader |
| getLogRRatio-method | Class IntensityData |
| getLogRRatio-method | Class NcdfIntensityReader |
| getMetadata | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getMetadata-method | Class ScanAnotationDataFrame |
| getMetadata-method | Class ScanAnotationSQLite |
| getMetadata-method | Class SnpAnotationDataFrame |
| getMetadata-method | Class SnpAnotationSQLite |
| getNodeDescription | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getNodeDescription-method | Class GdsReader |
| getobj | Get an R object stored in an Rdata file |
| getPosition | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getPosition-method | Class GdsGenotypeReader |
| getPosition-method | Class GdsIntensityReader |
| getPosition-method | Class GenotypeData |
| getPosition-method | Class GenotypeIterator |
| getPosition-method | Class IntensityData |
| getPosition-method | Class MatrixGenotypeReader |
| getPosition-method | Class NcdfGenotypeReader |
| getPosition-method | Class NcdfIntensityReader |
| getPosition-method | Class SnpAnotationDataFrame |
| getPosition-method | Class SnpAnotationSQLite |
| getQuality | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getQuality-method | Class GdsIntensityReader |
| getQuality-method | Class IntensityData |
| getQuality-method | Class NcdfIntensityReader |
| getQuery | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getQuery-method | Class ScanAnotationSQLite |
| getQuery-method | Class SnpAnotationSQLite |
| getScanAnnotation | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getScanAnnotation-method | Class GenotypeData |
| getScanID | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getScanID-method | Class GdsGenotypeReader |
| getScanID-method | Class GdsIntensityReader |
| getScanID-method | Class GenotypeData |
| getScanID-method | Class IntensityData |
| getScanID-method | Class MatrixGenotypeReader |
| getScanID-method | Class NcdfGenotypeReader |
| getScanID-method | Class NcdfIntensityReader |
| getScanID-method | Class ScanAnotationDataFrame |
| getScanID-method | Class ScanAnotationSQLite |
| getScanVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getScanVariable-method | Class GenotypeData |
| getScanVariable-method | Class IntensityData |
| getScanVariableNames | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getScanVariableNames-method | Class GenotypeData |
| getScanVariableNames-method | Class IntensityData |
| getSex | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getSex-method | Class GenotypeData |
| getSex-method | Class IntensityData |
| getSex-method | Class ScanAnotationDataFrame |
| getSex-method | Class ScanAnotationSQLite |
| getSnpAnnotation | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getSnpAnnotation-method | Class GenotypeData |
| getSnpID | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getSnpID-method | Class GdsGenotypeReader |
| getSnpID-method | Class GdsIntensityReader |
| getSnpID-method | Class GenotypeData |
| getSnpID-method | Class GenotypeIterator |
| getSnpID-method | Class IntensityData |
| getSnpID-method | Class MatrixGenotypeReader |
| getSnpID-method | Class NcdfGenotypeReader |
| getSnpID-method | Class NcdfIntensityReader |
| getSnpID-method | Class SnpAnotationDataFrame |
| getSnpID-method | Class SnpAnotationSQLite |
| getSnpVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getSnpVariable-method | Class GenotypeData |
| getSnpVariable-method | Class GenotypeIterator |
| getSnpVariable-method | Class IntensityData |
| getSnpVariableNames | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getSnpVariableNames-method | Class GenotypeData |
| getSnpVariableNames-method | Class IntensityData |
| getVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getVariable-method | Class GdsGenotypeReader |
| getVariable-method | Class GdsIntensityReader |
| getVariable-method | Class GdsReader |
| getVariable-method | Class GenotypeData |
| getVariable-method | Class IntensityData |
| getVariable-method | Class NcdfGenotypeReader |
| getVariable-method | Class NcdfIntensityReader |
| getVariable-method | Class NcdfReader |
| getVariable-method | Class ScanAnotationDataFrame |
| getVariable-method | Class ScanAnotationSQLite |
| getVariable-method | Class SnpAnotationDataFrame |
| getVariable-method | Class SnpAnotationSQLite |
| getVariableNames | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getVariableNames-method | Class GdsReader |
| getVariableNames-method | Class NcdfReader |
| getVariableNames-method | Class ScanAnotationDataFrame |
| getVariableNames-method | Class ScanAnotationSQLite |
| getVariableNames-method | Class SnpAnotationDataFrame |
| getVariableNames-method | Class SnpAnotationSQLite |
| getX | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getX-method | Class GdsIntensityReader |
| getX-method | Class IntensityData |
| getX-method | Class NcdfIntensityReader |
| getY | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getY-method | Class GdsIntensityReader |
| getY-method | Class IntensityData |
| getY-method | Class NcdfIntensityReader |
| gwasExactHW | Defunct Functions in Package 'GWASTools' |
| GWASTools | Tools for Genome Wide Association Studies |
| GWASTools-defunct | Defunct Functions in Package 'GWASTools' |
-- H --
| hasBAlleleFreq | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| hasBAlleleFreq-method | Class GdsIntensityReader |
| hasBAlleleFreq-method | Class IntensityData |
| hasBAlleleFreq-method | Class NcdfIntensityReader |
| hasCoordVariable | Class NcdfReader |
| hasCoordVariable-method | Class NcdfReader |
| hasLogRRatio | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| hasLogRRatio-method | Class GdsIntensityReader |
| hasLogRRatio-method | Class IntensityData |
| hasLogRRatio-method | Class NcdfIntensityReader |
| hasQuality | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| hasQuality-method | Class GdsIntensityReader |
| hasQuality-method | Class IntensityData |
| hasQuality-method | Class NcdfIntensityReader |
| hasScanAnnotation | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| hasScanAnnotation-method | Class GenotypeData |
| hasScanAnnotation-method | Class IntensityData |
| hasScanVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| hasScanVariable-method | Class GenotypeData |
| hasScanVariable-method | Class IntensityData |
| hasSex | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| hasSex-method | Class GenotypeData |
| hasSex-method | Class IntensityData |
| hasSex-method | Class ScanAnotationDataFrame |
| hasSex-method | Class ScanAnotationSQLite |
| hasSnpAnnotation | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| hasSnpAnnotation-method | Class GenotypeData |
| hasSnpAnnotation-method | Class IntensityData |
| hasSnpVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| hasSnpVariable-method | Class GenotypeData |
| hasSnpVariable-method | Class IntensityData |
| hasVariable | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| hasVariable-method | Class GdsReader |
| hasVariable-method | Class GenotypeData |
| hasVariable-method | Class IntensityData |
| hasVariable-method | Class NcdfReader |
| hasVariable-method | Class ScanAnotationDataFrame |
| hasVariable-method | Class ScanAnotationSQLite |
| hasVariable-method | Class SnpAnotationDataFrame |
| hasVariable-method | Class SnpAnotationSQLite |
| hasX | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| hasX-method | Class GdsIntensityReader |
| hasX-method | Class IntensityData |
| hasX-method | Class NcdfIntensityReader |
| hasY | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| hasY-method | Class GdsIntensityReader |
| hasY-method | Class IntensityData |
| hasY-method | Class NcdfIntensityReader |
| hetByScanChrom | Heterozygosity rates by scan and chromosome |
| hetBySnpSex | Heterozygosity by SNP and sex |
| HLA | HLA region base positions |
| HLA.hg18 | HLA region base positions |
| HLA.hg19 | HLA region base positions |
| HLA.hg38 | HLA region base positions |
-- I --
| ibdAreasDraw | Plot theoretical and observed identity by descent values and assign relationships |
| ibdAssignRelatedness | Plot theoretical and observed identity by descent values and assign relationships |
| ibdAssignRelatednessKing | Plot theoretical and observed identity by descent values and assign relationships |
| ibdPlot | Plot theoretical and observed identity by descent values and assign relationships |
| imputedDosageFile | Create and check a GDS or NetCDF file with imputed dosages |
| IntensityData | Class IntensityData |
| IntensityData-class | Class IntensityData |
| intensityOutliersPlot | Plot mean intensity and highlight outliers |
| iterateFilter | Class GenotypeIterator |
| iterateFilter-method | Class GenotypeIterator |
-- K --
| kingIBS0FSCI | Plot theoretical and observed identity by descent values and assign relationships |
-- L --
| lastFilter | Class GenotypeIterator |
| lastFilter-method | Class GenotypeIterator |
| lastFilter<- | Class GenotypeIterator |
| lastFilter<--method | Class GenotypeIterator |
-- M --
| manhattanPlot | Manhattan plot for genome wide association tests |
| MatrixGenotypeReader | Class MatrixGenotypeReader |
| MatrixGenotypeReader-class | Class MatrixGenotypeReader |
| MchromCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| MchromCode-method | Class GdsGenotypeReader |
| MchromCode-method | Class GdsIntensityReader |
| MchromCode-method | Class GenotypeData |
| MchromCode-method | Class IntensityData |
| MchromCode-method | Class MatrixGenotypeReader |
| MchromCode-method | Class NcdfGenotypeReader |
| MchromCode-method | Class NcdfIntensityReader |
| MchromCode-method | Class SnpAnotationDataFrame |
| MchromCode-method | Class SnpAnotationSQLite |
| meanIntensityByScanChrom | Calculate Means and Standard Deviations of Intensities |
| meanSdByChromWindow | Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation |
| medianSdOverAutosomes | Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation |
| mendelErr | Mendelian Error Checking |
| mendelList | Mendelian Error Checking |
| mendelListAsDataFrame | Mendelian Error Checking |
| minorAlleleDetectionAccuracy | Functions to check discordance and allelic dosage correlation across datasets |
| missingGenotypeByScanChrom | Missing Counts per Scan per Chromosome |
| missingGenotypeBySnpSex | Missing Counts per SNP by Sex |
-- N --
| ncdfAddData | Defunct Functions in Package 'GWASTools' |
| ncdfAddIntensity | Defunct Functions in Package 'GWASTools' |
| ncdfCheckGenotype | Defunct Functions in Package 'GWASTools' |
| ncdfCheckIntensity | Defunct Functions in Package 'GWASTools' |
| ncdfCreate | Defunct Functions in Package 'GWASTools' |
| NcdfGenotypeReader | Class NcdfGenotypeReader |
| NcdfGenotypeReader-class | Class NcdfGenotypeReader |
| ncdfImputedDosage | Defunct Functions in Package 'GWASTools' |
| NcdfIntensityReader | Class NcdfIntensityReader |
| NcdfIntensityReader-class | Class NcdfIntensityReader |
| NcdfReader | Class NcdfReader |
| NcdfReader-class | Class NcdfReader |
| ncdfSetMissingGenotypes | Defunct Functions in Package 'GWASTools' |
| ncdfSubset | Defunct Functions in Package 'GWASTools' |
| ncdfSubsetCheck | Defunct Functions in Package 'GWASTools' |
| nscan | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| nscan-method | Class GdsGenotypeReader |
| nscan-method | Class GdsIntensityReader |
| nscan-method | Class GenotypeData |
| nscan-method | Class IntensityData |
| nscan-method | Class MatrixGenotypeReader |
| nscan-method | Class NcdfGenotypeReader |
| nscan-method | Class NcdfIntensityReader |
| nscan-method | Class ScanAnotationSQLite |
| nsnp | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| nsnp-method | Class GdsGenotypeReader |
| nsnp-method | Class GdsIntensityReader |
| nsnp-method | Class GenotypeData |
| nsnp-method | Class IntensityData |
| nsnp-method | Class MatrixGenotypeReader |
| nsnp-method | Class NcdfGenotypeReader |
| nsnp-method | Class NcdfIntensityReader |
| nsnp-method | Class SnpAnotationSQLite |
-- O --
| open-method | Class GdsReader |
| open-method | Class GenotypeData |
| open-method | Class IntensityData |
| open-method | Class NcdfReader |
| open-method | Class ScanAnotationSQLite |
| open-method | Class SnpAnotationSQLite |
-- P --
| pasteSorted | Paste two vectors sorted pairwise |
| pcaSnpFilters | Regions of SNP-PC correlation to filter for Principal Component Analysis |
| 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 |
| 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 pedigree. |
| pedigreePairwiseRelatedness | Assign relatedness from pedigree data |
| plinkCheck | Utilities to create and check PLINK files |
| plinkToNcdf | Defunct Functions in Package 'GWASTools' |
| plinkWrite | Utilities to create and check PLINK files |
| pseudoautoIntensityPlot | Plot B Allele Frequency and Log R Ratio for the X and Y chromosomes, overlaying XY SNPs |
| pseudoautosomal | Pseudoautosomal region base positions |
| pseudoautosomal.hg18 | Pseudoautosomal region base positions |
| pseudoautosomal.hg19 | Pseudoautosomal region base positions |
| pseudoautosomal.hg38 | Pseudoautosomal region base positions |
-- Q --
| qqPlot | QQ plot for genome wide assocation studies |
| qualityScoreByScan | Mean and median quality score for scans |
| qualityScoreBySnp | Mean and median quality score for SNPs |
-- R --
| readWriteFirst | Read and write the first n lines of a file |
| relationsMeanVar | Mean and Variance information for full-sibs, half-sibs, first-cousins |
| resetIterator | Class GenotypeIterator |
| resetIterator-method | Class GenotypeIterator |
-- S --
| saveas | Save an R object with a new name |
| ScanAnnotationDataFrame | Class ScanAnotationDataFrame |
| ScanAnnotationDataFrame-class | Class ScanAnotationDataFrame |
| ScanAnnotationSQLite | Class ScanAnotationSQLite |
| ScanAnnotationSQLite-class | Class ScanAnotationSQLite |
| sdByScanChromWindow | Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation |
| setMissingGenotypes | Write a new netCDF or GDS file, setting certain SNPs to missing |
| show-method | Class GdsReader |
| show-method | Class GenotypeData |
| show-method | Class IntensityData |
| show-method | Class MatrixGenotypeReader |
| show-method | Class NcdfReader |
| show-method | Class ScanAnotationSQLite |
| show-method | Class SnpAnotationSQLite |
| simulateGenotypeMatrix | Simulate Genotype or Intensity Matrix & Load into GDS/NetCDF File |
| simulateIntensityMatrix | Simulate Genotype or Intensity Matrix & Load into GDS/NetCDF File |
| SnpAnnotationDataFrame | Class SnpAnotationDataFrame |
| SnpAnnotationDataFrame-class | Class SnpAnotationDataFrame |
| SnpAnnotationSQLite | Class SnpAnotationSQLite |
| SnpAnnotationSQLite-class | Class SnpAnotationSQLite |
| snpCorrelationPlot | SNP correlation plot |
| snpFilter | Class GenotypeIterator |
| snpFilter-method | Class GenotypeIterator |
-- V --
| vcfCheck | Utility to write VCF file |
| vcfWrite | Utility to write VCF file |
-- W --
| writeAnnotation | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| writeAnnotation-method | Class ScanAnotationSQLite |
| writeAnnotation-method | Class SnpAnotationSQLite |
| writeMetadata | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| writeMetadata-method | Class ScanAnotationSQLite |
| writeMetadata-method | Class SnpAnotationSQLite |
-- X --
| XchromCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| XchromCode-method | Class GdsGenotypeReader |
| XchromCode-method | Class GdsIntensityReader |
| XchromCode-method | Class GenotypeData |
| XchromCode-method | Class IntensityData |
| XchromCode-method | Class MatrixGenotypeReader |
| XchromCode-method | Class NcdfGenotypeReader |
| XchromCode-method | Class NcdfIntensityReader |
| XchromCode-method | Class SnpAnotationDataFrame |
| XchromCode-method | Class SnpAnotationSQLite |
| XYchromCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| XYchromCode-method | Class GdsGenotypeReader |
| XYchromCode-method | Class GdsIntensityReader |
| XYchromCode-method | Class GenotypeData |
| XYchromCode-method | Class IntensityData |
| XYchromCode-method | Class MatrixGenotypeReader |
| XYchromCode-method | Class NcdfGenotypeReader |
| XYchromCode-method | Class NcdfIntensityReader |
| XYchromCode-method | Class SnpAnotationDataFrame |
| XYchromCode-method | Class SnpAnotationSQLite |
-- Y --
| YchromCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| YchromCode-method | Class GdsGenotypeReader |
| YchromCode-method | Class GdsIntensityReader |
| YchromCode-method | Class GenotypeData |
| YchromCode-method | Class IntensityData |
| YchromCode-method | Class MatrixGenotypeReader |
| YchromCode-method | Class NcdfGenotypeReader |
| YchromCode-method | Class NcdfIntensityReader |
| YchromCode-method | Class SnpAnotationDataFrame |
| YchromCode-method | Class SnpAnotationSQLite |