Man pages for smgogarten/GWASTools
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 |
| anomIdentifyLowQuality | Identify low quality samples |
| anomSegStats | Calculate LRR and BAF statistics for anomalous segments |
| apartSnpSelection | Random selection of SNPs |
| assocCoxPH | Cox proportional hazards |
| assocRegression | Association testing with regression |
| BAFfromClusterMeans | B Allele Frequency & Log R Ratio Calculation |
| BAFfromGenotypes | B Allele Frequency & Log R Ratio Calculation |
| batchTest | Batch Effects of Genotyping |
| centromeres | Centromere base positions |
| chromIntensityPlot | Plot B Allele Frequency and/or Log R Ratio, R or Theta values... |
| convertNcdfGds | Convert between NetCDF and GDS format |
| createDataFile | Write genotypic calls and/or associated metrics to a GDS or... |
| defunct | Defunct Functions in Package 'GWASTools' |
| duplicateDiscordance | Duplicate discordance |
| duplicateDiscordanceAcrossDatasets | Functions to check discordance and allelic dosage correlation... |
| duplicateDiscordanceProbability | Probability of duplicate discordance |
| exactHWE | Hardy-Weinberg Equilibrium testing |
| findBAFvariance | Find chromosomal areas with high BAlleleFreq (or LogRRatio)... |
| GdsGenotypeReader-class | Class GdsGenotypeReader |
| GdsIntensityReader-class | Class GdsIntensityReader |
| GdsReader-class | Class GdsReader |
| gdsSubset | Write a subset of data in a GDS file to a new GDS file |
| genoClusterPlot | SNP cluster plots |
| GenotypeData-class | Class GenotypeData |
| GenotypeIterator-class | Class GenotypeIterator |
| genotypeToCharacter | Convert number of A alleles to character genotypes |
| getobj | Get an R object stored in an Rdata file |
| getVariable | Accessors for variables in GenotypeData and IntensityData... |
| GWASTools-package | Tools for Genome Wide Association Studies |
| hetByScanChrom | Heterozygosity rates by scan and chromosome |
| hetBySnpSex | Heterozygosity by SNP and sex |
| HLA | HLA region base positions |
| ibdPlot | Plot theoretical and observed identity by descent values and... |
| imputedDosageFile | Create and check a GDS or NetCDF file with imputed dosages |
| IntensityData-class | Class IntensityData |
| intensityOutliersPlot | Plot mean intensity and highlight outliers |
| manhattanPlot | Manhattan plot for genome wide association tests |
| MatrixGenotypeReader-class | Class MatrixGenotypeReader |
| meanIntensityByScanChrom | Calculate Means and Standard Deviations of Intensities |
| mendelErr | Mendelian Error Checking |
| mendelList | Mendelian Error Checking |
| missingGenotypeByScanChrom | Missing Counts per Scan per Chromosome |
| missingGenotypeBySnpSex | Missing Counts per SNP by Sex |
| NcdfGenotypeReader-class | Class NcdfGenotypeReader |
| NcdfIntensityReader-class | Class NcdfIntensityReader |
| NcdfReader-class | Class NcdfReader |
| pasteSorted | Paste two vectors sorted pairwise |
| pcaSnpFilters | Regions of SNP-PC correlation to filter for Principal... |
| 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... |
| pedigreePairwiseRelatedness | Assign relatedness from pedigree data |
| plinkUtils | Utilities to create and check PLINK files |
| pseudoautoIntensityPlot | Plot B Allele Frequency and Log R Ratio for the X and Y... |
| pseudoautosomal | 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,... |
| saveas | Save an R object with a new name |
| ScanAnnotationDataFrame-class | Class ScanAnotationDataFrame |
| ScanAnnotationSQLite-class | Class ScanAnotationSQLite |
| setMissingGenotypes | Write a new netCDF or GDS file, setting certain SNPs to... |
| simulateGenotypeMatrix | Simulate Genotype or Intensity Matrix & Load into GDS/NetCDF... |
| SnpAnnotationDataFrame-class | Class SnpAnotationDataFrame |
| SnpAnnotationSQLite-class | Class SnpAnotationSQLite |
| snpCorrelationPlot | SNP correlation plot |
| snpStats | Utilities for snpStats |
| vcfWrite | Utility to write VCF file |
