Name Mode Size
..
BAFfromClusterMeans.Rd 100755 2 kb
BAFfromGenotypes.Rd 100755 4 kb
GWASTools-package.Rd 100755 2 kb
GdsGenotypeReader-class.Rd 100755 8 kb
GdsIntensityReader-class.Rd 100644 8 kb
GdsReader-class.Rd 100755 4 kb
GenotypeData-class.Rd 100755 12 kb
GenotypeIterator-class.Rd 100644 4 kb
HLA.Rd 100755 1 kb
IntensityData-class.Rd 100755 10 kb
MatrixGenotypeReader-class.Rd 100755 6 kb
NcdfGenotypeReader-class.Rd 100755 6 kb
NcdfIntensityReader-class.Rd 100755 8 kb
NcdfReader-class.Rd 100755 4 kb
ScanAnnotationDataFrame-class.Rd 100755 5 kb
ScanAnnotationSQLite-class.Rd 100755 5 kb
SnpAnnotationDataFrame-class.Rd 100755 7 kb
SnpAnnotationSQLite-class.Rd 100755 8 kb
alleleFrequency.Rd 100755 2 kb
allequal.Rd 100755 1 kb
anomDetectBAF.Rd 100755 13 kb
anomDetectLOH.Rd 100755 13 kb
anomIdentifyLowQuality.Rd 100755 6 kb
anomSegStats.Rd 100755 13 kb
apartSnpSelection.Rd 100755 2 kb
assocCoxPH.Rd 100644 6 kb
assocRegression.Rd 100644 8 kb
batchTest.Rd 100755 5 kb
centromeres.Rd 100755 1 kb
chromIntensityPlot.Rd 100755 4 kb
convertNcdfGds.Rd 100755 2 kb
createDataFile.Rd 100644 15 kb
defunct.Rd 100755 2 kb
duplicateDiscordance.Rd 100755 4 kb
duplicateDiscordanceAcrossDatasets.Rd 100755 12 kb
duplicateDiscordanceProbability.Rd 100755 2 kb
exactHWE.Rd 100755 3 kb
findBAFvariance.Rd 100755 7 kb
gdsSubset.Rd 100644 4 kb
genoClusterPlot.Rd 100755 4 kb
genotypeToCharacter.Rd 100644 1 kb
getVariable.Rd 100755 4 kb
getobj.Rd 100755 1 kb
hetByScanChrom.Rd 100755 2 kb
hetBySnpSex.Rd 100755 2 kb
ibdPlot.Rd 100755 8 kb
imputedDosageFile.Rd 100644 11 kb
intensityOutliersPlot.Rd 100755 3 kb
manhattanPlot.Rd 100755 3 kb
meanIntensityByScanChrom.Rd 100755 2 kb
mendelErr.Rd 100755 5 kb
mendelList.Rd 100755 3 kb
missingGenotypeByScanChrom.Rd 100755 2 kb
missingGenotypeBySnpSex.Rd 100755 2 kb
pasteSorted.Rd 100644 0 kb
pcaSnpFilters.Rd 100755 1 kb
pedigreeCheck.Rd 100755 7 kb
pedigreeDeleteDuplicates.Rd 100755 2 kb
pedigreeMaxUnrelated.Rd 100755 5 kb
pedigreePairwiseRelatedness.Rd 100755 4 kb
plinkUtils.Rd 100755 5 kb
pseudoautoIntensityPlot.Rd 100755 2 kb
pseudoautosomal.Rd 100755 1 kb
qqPlot.Rd 100755 2 kb
qualityScoreByScan.Rd 100755 2 kb
qualityScoreBySnp.Rd 100755 2 kb
readWriteFirst.Rd 100755 1 kb
relationsMeanVar.Rd 100755 2 kb
saveas.Rd 100755 1 kb
setMissingGenotypes.Rd 100644 2 kb
simulateGenotypeMatrix.Rd 100755 4 kb
snpCorrelationPlot.Rd 100755 2 kb
snpStats.Rd 100755 3 kb
vcfWrite.Rd 100644 4 kb
README.md
# GWASTools Tools for Genome Wide Association Studies This package contains tools for facilitating cleaning (quality control and quality assurance) and analysis of GWAS data. ## Bioconductor [http://www.bioconductor.org/packages/release/bioc/html/GWASTools.html](http://www.bioconductor.org/packages/release/bioc/html/GWASTools.html) * Tutorials * [Data formats in GWASTools](http://bioconductor.org/packages/release/bioc/vignettes/GWASTools/inst/doc/Formats.pdf) * [GWAS Data Cleaning](http://bioconductor.org/packages/release/bioc/vignettes/GWASTools/inst/doc/DataCleaning.pdf) * [Reference manual](http://www.bioconductor.org/packages/release/bioc/manuals/GWASTools/man/GWASTools.pdf) * [News](http://bioconductor.org/packages/release/bioc/news/GWASTools/NEWS) ## Installation ```R if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("GWASTools") ```