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GWASTools (version 1.12.2)

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

1.12.2

License

Artistic-2.0

Maintainer

Stephanie M Gogarten

Last Published

February 15th, 2017

Functions in GWASTools (1.12.2)

convertVcfGds

Conversion from VCF to GDS
anomIdentifyLowQuality

Identify low quality samples
anomSegStats

Calculate LRR and BAF statistics for anomalous segments
createDataFile

Write genotypic calls and/or associated metrics to a GDS or netCDF file.
duplicateDiscordance

Duplicate discordance
duplicateDiscordanceAcrossDatasets

Duplicate discordance across datasets
hetByScanChrom

Heterozygosity rates by scan and chromosome
hetBySnpSex

Heterozygosity by SNP and sex
intensityOutliersPlot

Plot mean intensity and highlight outliers
manhattanPlot

Manhattan plot for genome wide association tests
NcdfIntensityReader

Class NcdfIntensityReader
pedigreePairwiseRelatedness

Assign relatedness from pedigree data
NcdfReader

Class NcdfReader
pedigreeMaxUnrelated

Find a maximal set of unrelated individuals in a subset of a pedigree.
qualityScoreBySnp

Mean and median quality score for SNPs
readWriteFirst

Read and write the first n lines of a file
asSnpMatrix

Utilities for snpStats
vcfWrite

Utility to write VCF file
anomDetectBAF

BAF Method for Chromosome Anomaly Detection
anomDetectLOH

LOH Method for Chromosome Anomaly Detection
BAFfromClusterMeans

B Allele Frequency & Log R Ratio Calculation
gwasExactHW

Hardy-Weinberg Equilibrium testing
BAFfromGenotypes

B Allele Frequency & Log R Ratio Calculation
GWASTools-package

Tools for Genome Wide Association Studies
ncdfAddData

Write genotypic calls and/or associated metrics to a netCDF file - deprecated
ncdfCreate

Write genotypic calls and/or associated metrics to a netCDF file - deprecated
pedigreeCheck

Testing for internal consistency of pedigrees
pedigreeDeleteDuplicates

Remove duplicates from a pedigree
apartSnpSelection

Random selection of SNPs
assocTestCPH

Cox proportional hazards
GWASTools-defunct

Defunct Functions in Package GWASTools
GWASTools-deprecated

Deprecated functions in package ‘GWASTools’
setMissingGenotypes

Write a new netCDF or GDS file, setting certain SNPs to missing
gdsSubset

Write a subset of data in a GDS file to a new GDS file
simulateGenotypeMatrix

Simulate Genotype Matrix & Load into NetCDF File
genoClusterPlot

SNP cluster plots
genotypeToCharacter

Convert number of A alleles to character genotypes
GenotypeData-class

Class GenotypeData
MatrixGenotypeReader

Class MatrixGenotypeReader
qqPlot

QQ plot for genome wide assocation studies
ncdfImputedDosage

Create a NetCDF file with imputed dosages - deprecated
meanIntensityByScanChrom

Calculate Means \& Standard Deviations of Intensities
NcdfGenotypeReader

Class NcdfGenotypeReader
qualityScoreByScan

Mean and median quality score for scans
SnpAnnotationDataFrame

Class SnpAnotationDataFrame
simulateIntensityMatrix

Simulate Intensity Matrix & Load into NetCDF File
batchTest

Batch Effects of Genotyping
centromeres

Centromere base positions
GdsGenotypeReader

Class GdsGenotypeReader
gdsImputedDosage

Create and check a GDS file with imputed dosages - deprecated
getVariable

Accessors for variables in GenotypeData and IntensityData classes and their component classes
getobj

Get an R object stored in an Rdata file
missingGenotypeBySnpSex

Missing Counts per SNP by Sex
missingGenotypeByScanChrom

Missing Counts per Scan per Chromosome
plinkToNcdf

Create a netCDF file and annotation suitable for use in GWASTools from PLINK files
plinkUtils

Utilities to create and check PLINK files
ncdfSetMissingGenotypes

Write a new netCDF or GDS file, setting certain SNPs to missing - deprecated
ncdfSubset

Write a subset of data in a netCDF file to a new netCDF file
ScanAnnotationDataFrame

Class ScanAnotationDataFrame
ScanAnnotationSQLite

Class ScanAnotationSQLite
allequal

Test if two objects have the same elements
alleleFrequency

Allelic frequency
duplicateDiscordanceProbability

Probability of duplicate discordance
findBAFvariance

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

Mendelian Error Checking
mendelList

Mendelian Error Checking
pseudoautoIntensityPlot

Plot B Allele Frequency and Log R Ratio for the X and Y chromosomes, overlaying XY SNPs
pseudoautosomal

Pseudoautosomal region base positions
SnpAnnotationSQLite

Class SnpAnotationSQLite
snpCorrelationPlot

SNP correlation plot
assocTestFisherExact

Association tests
chromIntensityPlot

Plot B Allele Frequency and/or Log R Ratio, R or Theta values for samples by probe position on a chromosome
assocTestRegression

Association tests
convertNcdfGds

Convert between NetCDF and GDS format
GdsReader

Class GdsReader
GdsIntensityReader

Class GdsIntensityReader
HLA

HLA region base positions
ibdPlot

Plot theoretical and observed identity by descent values and assign relationships
imputedDosageFile

Create and check a GDS or NetCDF file with imputed dosages
pasteSorted

Paste two vectors sorted pairwise
pcaSnpFilters

Regions of SNP-PC correlation to filter for Principal Component Analysis
IntensityData-class

Class IntensityData
relationsMeanVar

Mean and Variance information for full-sibs, half-sibs, first-cousins
saveas

Save an R object with a new name