Name Mode Size
..
AllClasses.R 100755 11 kb
AllGenerics.R 100755 5 kb
BAFfromClusterMeans.R 100755 3 kb
BAFfromGenotypes.R 100755 6 kb
LOHfind.R 100755 8 kb
LOHselectAnoms.R 100755 7 kb
Methods-GdsGenotypeReader.R 100755 13 kb
Methods-GdsIntensityReader.R 100644 7 kb
Methods-GdsReader.R 100755 3 kb
Methods-GenotypeData.R 100755 10 kb
Methods-IntensityData.R 100755 9 kb
Methods-Iterator.R 100644 3 kb
Methods-MatrixGenotypeReader.R 100755 6 kb
Methods-NcdfGenotypeReader.R 100755 6 kb
Methods-NcdfIntensityReader.R 100755 7 kb
Methods-NcdfReader.R 100755 4 kb
Methods-ScanAnnotationDataFrame.R 100755 3 kb
Methods-ScanAnnotationSQLite.R 100755 7 kb
Methods-SnpAnnotationDataFrame.R 100755 5 kb
Methods-SnpAnnotationSQLite.R 100755 10 kb
alleleFrequency.R 100755 3 kb
anomDetectBAF.R 100755 0 kb
anomDetectLOH.R 100755 11 kb
anomFilterBAF.R 100755 39 kb
anomIdentifyLowQuality.R 100755 4 kb
anomSegStats.R 100755 19 kb
anomSegmentBAF.R 100755 4 kb
anomStatsPlot.R 100755 17 kb
apartSnpSelection.R 100755 2 kb
asVCF.R 100644 5 kb
assocCoxPH.R 100644 10 kb
assocRegression.R 100644 13 kb
batchChisqTest.R 100755 7 kb
batchFisherTest.R 100755 5 kb
checkGenotypeFile.R 100644 8 kb
checkImputedDosageFile.R 100644 13 kb
checkIntensityFile.R 100644 13 kb
chromIntensityPlot.R 100755 10 kb
convertNcdfGds.R 100755 8 kb
createAffyIntensityFile.R 100644 5 kb
createDataFile.R 100644 12 kb
createDataUtils.R 100644 10 kb
dupDosageCorAcrossDatasets.R 100644 9 kb
duplicateDiscordance.R 100755 9 kb
duplicateDiscordanceAcrossDatasets.R 100755 16 kb
duplicateDiscordanceProbability.R 100755 2 kb
exactHWE.R 100644 5 kb
findBAFvariance.R 100755 3 kb
findRelationsMeanVar.R 100755 3 kb
gdsSubset.R 100644 7 kb
gdsSubsetCheck.R 100644 7 kb
genoClusterPlot.R 100755 6 kb
genoClusterPlotByBatch.R 100755 4 kb
genotypeToCharacter.R 100644 2 kb
hetByScanChrom.R 100755 2 kb
hetBySnpSex.R 100755 1 kb
ibdAreasDraw.R 100755 3 kb
ibdAssignRelatedness.R 100755 5 kb
ibdPlot.R 100755 3 kb
imputedDosageFile.R 100644 19 kb
intensityOutliersPlot.R 100755 4 kb
manhattanPlot.R 100755 3 kb
meanIntensityByScanChrom.R 100755 5 kb
meanSdByChromWindow.R 100755 2 kb
medianSdOverAutosomes.R 100755 1 kb
mendelErr.R 100755 15 kb
missingGenotypeByScanChrom.R 100755 2 kb
missingGenotypeBySnpSex.R 100755 2 kb
pedigreeCheck.R 100755 13 kb
pedigreeDeleteDuplicates.R 100755 1 kb
pedigreeMaxUnrelated.R 100755 9 kb
pedigreePairwiseRelatedness.R 100755 16 kb
plinkUtils.R 100755 11 kb
pseudoautoIntensityPlot.R 100755 7 kb
qqPlot.R 100755 2 kb
qualityScoreByScan.R 100755 3 kb
qualityScoreBySnp.R 100755 2 kb
sdByScanChromWindow.R 100755 7 kb
setMissingGenotypes.R 100644 3 kb
simulateGenotypeMatrix.R 100755 2 kb
simulateIntensityMatrix.R 100755 3 kb
snpCorrelationPlot.R 100755 1 kb
snpStats.R 100755 1 kb
utils.R 100755 2 kb
vcfWrite.R 100644 13 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") ```