Man pages for smgogarten/GWASTools
Tools for Genome Wide Association Studies

alleleFrequencyAllelic frequency
allequalTest if two objects have the same elements
anomDetectBAFBAF Method for Chromosome Anomaly Detection
anomDetectLOHLOH Method for Chromosome Anomaly Detection
anomIdentifyLowQualityIdentify low quality samples
anomSegStatsCalculate LRR and BAF statistics for anomalous segments
apartSnpSelectionRandom selection of SNPs
assocCoxPHCox proportional hazards
assocRegressionAssociation testing with regression
BAFfromClusterMeansB Allele Frequency & Log R Ratio Calculation
BAFfromGenotypesB Allele Frequency & Log R Ratio Calculation
batchTestBatch Effects of Genotyping
centromeresCentromere base positions
chromIntensityPlotPlot B Allele Frequency and/or Log R Ratio, R or Theta values...
convertNcdfGdsConvert between NetCDF and GDS format
createDataFileWrite genotypic calls and/or associated metrics to a GDS or...
defunctDefunct Functions in Package 'GWASTools'
duplicateDiscordanceDuplicate discordance
duplicateDiscordanceAcrossDatasetsFunctions to check discordance and allelic dosage correlation...
duplicateDiscordanceProbabilityProbability of duplicate discordance
exactHWEHardy-Weinberg Equilibrium testing
findBAFvarianceFind chromosomal areas with high BAlleleFreq (or LogRRatio)...
GdsGenotypeReader-classClass GdsGenotypeReader
GdsIntensityReader-classClass GdsIntensityReader
GdsReader-classClass GdsReader
gdsSubsetWrite a subset of data in a GDS file to a new GDS file
genoClusterPlotSNP cluster plots
GenotypeData-classClass GenotypeData
genotypeToCharacterConvert number of A alleles to character genotypes
getobjGet an R object stored in an Rdata file
getVariableAccessors for variables in GenotypeData and IntensityData...
GWASTools-packageTools for Genome Wide Association Studies
hetByScanChromHeterozygosity rates by scan and chromosome
hetBySnpSexHeterozygosity by SNP and sex
HLAHLA region base positions
ibdPlotPlot theoretical and observed identity by descent values and...
imputedDosageFileCreate and check a GDS or NetCDF file with imputed dosages
IntensityData-classClass IntensityData
intensityOutliersPlotPlot mean intensity and highlight outliers
manhattanPlotManhattan plot for genome wide association tests
MatrixGenotypeReader-classClass MatrixGenotypeReader
meanIntensityByScanChromCalculate Means & Standard Deviations of Intensities
mendelErrMendelian Error Checking
mendelListMendelian Error Checking
missingGenotypeByScanChromMissing Counts per Scan per Chromosome
missingGenotypeBySnpSexMissing Counts per SNP by Sex
NcdfGenotypeReader-classClass NcdfGenotypeReader
NcdfIntensityReader-classClass NcdfIntensityReader
NcdfReader-classClass NcdfReader
pasteSortedPaste two vectors sorted pairwise
pcaSnpFiltersRegions of SNP-PC correlation to filter for Principal...
pedigreeCheckTesting for internal consistency of pedigrees
pedigreeDeleteDuplicatesRemove duplicates from a pedigree
pedigreeMaxUnrelatedFind a maximal set of unrelated individuals in a subset of a...
pedigreePairwiseRelatednessAssign relatedness from pedigree data
plinkUtilsUtilities to create and check PLINK files
pseudoautoIntensityPlotPlot B Allele Frequency and Log R Ratio for the X and Y...
pseudoautosomalPseudoautosomal region base positions
qqPlotQQ plot for genome wide assocation studies
qualityScoreByScanMean and median quality score for scans
qualityScoreBySnpMean and median quality score for SNPs
readWriteFirstRead and write the first n lines of a file
relationsMeanVarMean and Variance information for full-sibs, half-sibs,...
saveasSave an R object with a new name
ScanAnnotationDataFrame-classClass ScanAnotationDataFrame
ScanAnnotationSQLite-classClass ScanAnotationSQLite
setMissingGenotypesWrite a new netCDF or GDS file, setting certain SNPs to...
simulateGenotypeMatrixSimulate Genotype or Intensity Matrix & Load into GDS/NetCDF...
SnpAnnotationDataFrame-classClass SnpAnotationDataFrame
SnpAnnotationSQLite-classClass SnpAnotationSQLite
snpCorrelationPlotSNP correlation plot
snpStatsUtilities for snpStats
vcfWriteUtility to write VCF file
smgogarten/GWASTools documentation built on Nov. 7, 2017, 9:59 p.m.