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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

License

Artistic-2.0

Maintainer

Stephanie M Gogarten

Last Published

February 15th, 2017

Functions in GWASTools (1.18.0)

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