Tools for Genome Wide Association Studies


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Documentation for package ‘GWASTools’ version 1.2.1

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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

-- 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
assocTestCPH Cox proportional hazards
assocTestRegression Association tests

-- 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
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

-- D --

duplicateDiscordance Duplicate discordance
duplicateDiscordanceAcrossDatasets Duplicate discordance across datasets
duplicateDiscordanceProbability Probability of duplicate discordance

-- F --

findBAFvariance Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation

-- G --

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

-- H --

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

-- 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
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

-- 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 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

-- N --

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
ncdfSetMissingGenotypes Write a new netCDF file, setting certain SNPs to missing
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

-- O --

open-method Class GenotypeData
open-method Class IntensityData
open-method Class NcdfReader
open-method Class ScanAnotationSQLite
open-method Class SnpAnotationSQLite

-- P --

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
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
plinkCheck Utilities to create and check PLINK files
plinkToNcdf Create a netCDF file and annotation suitable for use in GWASTools from PLINK files
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

-- 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

-- 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
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

-- 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 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

-- Y --

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