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GWASTools (version 1.18.0)
Tools for Genome Wide Association Studies
Description
Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.
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Version
Version
1.18.0
1.16.1
1.14.2
1.12.2
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Version
1.18.0
License
Artistic-2.0
Maintainer
Stephanie M Gogarten
Last Published
January 1st, 1970
Functions in GWASTools (1.18.0)
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BAFfromClusterMeans
B Allele Frequency & Log R Ratio Calculation
gdsSubset
Write a subset of data in a GDS file to a new GDS file
anomIdentifyLowQuality
Identify low quality samples
GWASTools-defunct
Defunct Functions in Package ‘GWASTools’
asSnpMatrix
Utilities for snpStats
alleleFrequency
Allelic frequency
findBAFvariance
Find chromosomal areas with high BAlleleFreq (or LogRRatio) standard deviation
readWriteFirst
Read and write the first n lines of a file
pcaSnpFilters
Regions of SNP-PC correlation to filter for Principal Component Analysis
saveas
Save an R object with a new name
GdsIntensityReader
Class GdsIntensityReader
GenotypeData-class
Class GenotypeData
ScanAnnotationDataFrame
Class ScanAnotationDataFrame
NcdfGenotypeReader
Class NcdfGenotypeReader
anomDetectBAF
BAF Method for Chromosome Anomaly Detection
qualityScoreByScan
Mean and median quality score for scans
pseudoautoIntensityPlot
Plot B Allele Frequency and Log R Ratio for the X and Y chromosomes, overlaying XY SNPs
apartSnpSelection
Random selection of SNPs
relationsMeanVar
Mean and Variance information for full-sibs, half-sibs, first-cousins
anomSegStats
Calculate LRR and BAF statistics for anomalous segments
convertNcdfGds
Convert between NetCDF and GDS format
centromeres
Centromere base positions
genotypeToCharacter
Convert number of A alleles to character genotypes
mendelList
Mendelian Error Checking
exactHWE
Hardy-Weinberg Equilibrium testing
missingGenotypeByScanChrom
Missing Counts per Scan per Chromosome
assocCoxPH
Cox proportional hazards
genoClusterPlot
SNP cluster plots
duplicateDiscordanceAcrossDatasets
Functions to check discordance and allelic dosage correlation across datasets
mendelErr
Mendelian Error Checking
hetByScanChrom
Heterozygosity rates by scan and chromosome
vcfWrite
Utility to write VCF file
manhattanPlot
Manhattan plot for genome wide association tests
allequal
Test if two objects have the same elements
pseudoautosomal
Pseudoautosomal region base positions
pedigreeMaxUnrelated
Find a maximal set of unrelated individuals in a subset of a pedigree.
plinkToNcdf
Create a netCDF file and annotation suitable for use in GWASTools from PLINK files
qqPlot
QQ plot for genome wide assocation studies
plinkUtils
Utilities to create and check PLINK files
pasteSorted
Paste two vectors sorted pairwise
SnpAnnotationDataFrame
Class SnpAnotationDataFrame
SnpAnnotationSQLite
Class SnpAnotationSQLite
assocRegression
Association testing with regression
chromIntensityPlot
Plot B Allele Frequency and/or Log R Ratio, R or Theta values for samples by probe position on a chromosome
getobj
Get an R object stored in an Rdata file
hetBySnpSex
Heterozygosity by SNP and sex
GdsGenotypeReader
Class GdsGenotypeReader
BAFfromGenotypes
B Allele Frequency & Log R Ratio Calculation
MatrixGenotypeReader
Class MatrixGenotypeReader
ScanAnnotationSQLite
Class ScanAnotationSQLite
createDataFile
Write genotypic calls and/or associated metrics to a GDS or netCDF file.
duplicateDiscordanceProbability
Probability of duplicate discordance
meanIntensityByScanChrom
Calculate Means \& Standard Deviations of Intensities
GWASTools-package
Tools for Genome Wide Association Studies
IntensityData-class
Class IntensityData
simulateGenotypeMatrix
Simulate Genotype or Intensity Matrix & Load into GDS/NetCDF File
convertVcfGds
Conversion from VCF to GDS
pedigreePairwiseRelatedness
Assign relatedness from pedigree data
qualityScoreBySnp
Mean and median quality score for SNPs
NcdfIntensityReader
Class NcdfIntensityReader
GWASTools-deprecated
Deprecated functions in package ‘GWASTools’
getVariable
Accessors for variables in GenotypeData and IntensityData classes and their component classes
intensityOutliersPlot
Plot mean intensity and highlight outliers
duplicateDiscordance
Duplicate discordance
pedigreeDeleteDuplicates
Remove duplicates from a pedigree
GdsReader
Class GdsReader
HLA
HLA region base positions
NcdfReader
Class NcdfReader
ibdPlot
Plot theoretical and observed identity by descent values and assign relationships
anomDetectLOH
LOH Method for Chromosome Anomaly Detection
imputedDosageFile
Create and check a GDS or NetCDF file with imputed dosages
missingGenotypeBySnpSex
Missing Counts per SNP by Sex
pedigreeCheck
Testing for internal consistency of pedigrees
snpCorrelationPlot
SNP correlation plot
batchTest
Batch Effects of Genotyping
setMissingGenotypes
Write a new netCDF or GDS file, setting certain SNPs to missing