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A B C D F G H I M N O P Q R S W X Y
| GWASTools-package | Tools for Genome Wide Association Studies |
| 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 |
| assocTestCPH | Cox proportional hazards |
| assocTestRegression | Association tests |
| 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 |
| centromeres | Centromere base positions |
| centromeres.hg18 | Centromere base positions |
| centromeres.hg19 | Centromere base positions |
| 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 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 |
| duplicateDiscordance | Duplicate discordance |
| duplicateDiscordanceAcrossDatasets | Duplicate discordance across datasets |
| duplicateDiscordanceProbability | Probability of duplicate discordance |
| findBAFvariance | Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation |
| genoClusterPlot | SNP cluster plots |
| genoClusterPlotByBatch | SNP cluster plots |
| GenotypeData | Class GenotypeData |
| GenotypeData-class | Class GenotypeData |
| 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 | Class NcdfReader |
| getAttribute-method | Class NcdfReader |
| getBAlleleFreq | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getBAlleleFreq-method | Class IntensityData |
| getBAlleleFreq-method | Class NcdfIntensityReader |
| getChromosome | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getChromosome-method | Class GenotypeData |
| getChromosome-method | Class IntensityData |
| getChromosome-method | Class MatrixGenotypeReader |
| getChromosome-method | Class NcdfGenotypeReader |
| getChromosome-method | Class NcdfIntensityReader |
| getChromosome-method | Class SnpAnotationDataFrame |
| getChromosome-method | Class SnpAnotationSQLite |
| getDimensionNames | Class NcdfReader |
| getDimensionNames-method | Class NcdfReader |
| getGenotype | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getGenotype-method | Class GenotypeData |
| getGenotype-method | Class MatrixGenotypeReader |
| getGenotype-method | Class NcdfGenotypeReader |
| getLogRRatio | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| 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 |
| 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 GenotypeData |
| 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 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 |
| getScanID | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| 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 |
| getSnpID | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getSnpID-method | Class GenotypeData |
| 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 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 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 | Class NcdfReader |
| 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 IntensityData |
| getX-method | Class NcdfIntensityReader |
| getY | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| getY-method | Class IntensityData |
| getY-method | Class NcdfIntensityReader |
| gwasExactHW | Hardy-Weinberg Equilibrium testing |
| GWASTools | Tools for Genome Wide Association Studies |
| hasBAlleleFreq | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| 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 IntensityData |
| hasLogRRatio-method | Class NcdfIntensityReader |
| hasQuality | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| 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 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 IntensityData |
| hasX-method | Class NcdfIntensityReader |
| hasY | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| 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 |
| ibdAreasDraw | Plot theoretical and observed identity by descent values and assign relationships |
| ibdAssignRelatedness | Plot theoretical and observed identity by descent values and assign relationships |
| ibdPlot | Plot theoretical and observed identity by descent values and assign relationships |
| IntensityData | Class IntensityData |
| IntensityData-class | Class IntensityData |
| intensityOutliersPlot | Plot mean intensity and highlight outliers |
| 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 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 & 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 |
| missingGenotypeByScanChrom | Missing Counts per Scan per Chromosome |
| missingGenotypeBySnpSex | Missing Counts per SNP by Sex |
| ncdfAddData | Write genotypic calls and/or associated metrics to a netCDF file |
| ncdfAddIntensity | Write genotypic calls and/or associated metrics to a netCDF file |
| ncdfCheckGenotype | Write genotypic calls and/or associated metrics to a netCDF file |
| ncdfCheckIntensity | Write genotypic calls and/or associated metrics to a netCDF file |
| ncdfCreate | Write genotypic calls and/or associated metrics to a netCDF file. |
| NcdfGenotypeReader | Class NcdfGenotypeReader |
| NcdfGenotypeReader-class | Class NcdfGenotypeReader |
| NcdfIntensityReader | Class NcdfIntensityReader |
| NcdfIntensityReader-class | Class NcdfIntensityReader |
| NcdfReader | Class NcdfReader |
| NcdfReader-class | Class NcdfReader |
| ncdfSubset | Write a subset of data in a netCDF file to a new netCDF file |
| ncdfSubsetCheck | Write a subset of data in a netCDF file to a new netCDF file |
| nscan | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| 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 GenotypeData |
| nsnp-method | Class IntensityData |
| nsnp-method | Class MatrixGenotypeReader |
| nsnp-method | Class NcdfGenotypeReader |
| nsnp-method | Class NcdfIntensityReader |
| nsnp-method | Class SnpAnotationSQLite |
| open-method | Class GenotypeData |
| open-method | Class IntensityData |
| open-method | Class NcdfReader |
| open-method | Class ScanAnotationSQLite |
| open-method | Class SnpAnotationSQLite |
| pedigreeCheck | Testing for internal consistency of pedigrees |
| pedigreeClean | Basic pedigree data checking |
| pedigreeDeleteDuplicates | Identify and remove duplicates from a pedigree |
| pedigreeFindDuplicates | Identify and remove duplicates from a pedigree |
| pedigreePairwiseRelatedness | Calculate theoretical pairwise relatedness values from pedigrees |
| 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 |
| 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, first-cousins |
| 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 |
| 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 Matrix & Load into NetCDF File |
| simulateIntensityMatrix | Simulate Intensity Matrix & Load into NetCDF File |
| SnpAnnotationDataFrame | Class SnpAnotationDataFrame |
| SnpAnnotationDataFrame-class | Class SnpAnotationDataFrame |
| SnpAnnotationSQLite | Class SnpAnotationSQLite |
| SnpAnnotationSQLite-class | Class SnpAnotationSQLite |
| snpCorrelationPlot | SNP correlation plot |
| 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 |
| XchromCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| 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 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 |
| YchromCode | Accessors for variables in GenotypeData and IntensityData classes and their component classes |
| 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 |