Package: GWASTools
Version: 1.12.2
Type: Package
Title: 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.
Author: Stephanie M. Gogarten, Cathy Laurie, Tushar Bhangale, Matthew P. Conomos, Cecelia Laurie, Caitlin McHugh, Ian Painter, Xiuwen Zheng, Jess Shen, Rohit Swarnkar, Adrienne Stilp
Maintainer: Stephanie M. Gogarten <sdmorris@u.washington.edu>, Adrienne Stilp <amstilp@u.washington.edu>
Depends: Biobase, ncdf, gdsfmt
Imports: methods, DBI, RSQLite, GWASExactHW, DNAcopy, survival,
        sandwich, lmtest, quantsmooth
Suggests: GWASdata, BiocGenerics, RUnit, SNPRelate, snpStats,
        VariantAnnotation
License: Artistic-2.0
LazyData: yes
biocViews: SNP, GeneticVariability, QualityControl, Microarray
Collate: utils.R AllGenerics.R AllClasses.R genotypeToCharacter.R
        Methods-ScanAnnotationDataFrame.R
        Methods-SnpAnnotationDataFrame.R Methods-ScanAnnotationSQLite.R
        Methods-SnpAnnotationSQLite.R Methods-NcdfReader.R
        Methods-NcdfGenotypeReader.R Methods-NcdfIntensityReader.R
        Methods-GdsReader.R Methods-GdsGenotypeReader.R
        Methods-GdsIntensityReader.R Methods-MatrixGenotypeReader.R
        Methods-GenotypeData.R Methods-IntensityData.R createDataFile.R
        createAffyIntensityFile.R checkGenotypeFile.R
        checkIntensityFile.R setMissingGenotypes.R imputedDosageFile.R
        checkImputedDosageFile.R ncdfSubset.R ncdfSubsetCheck.R
        gdsSubset.R gdsSubsetCheck.R ncdfCreate.R ncdfAddData.R
        ncdfAddIntensity.R ncdfCheckIntensity.R ncdfCheckGenotype.R
        ncdfSetMissingGenotypes.R gdsSetMissingGenotypes.R
        ncdfImputedDosage.R gdsImputedDosage.R gdsCheckImputedDosage.R
        plinkUtils.R snpStats.R vcfWrite.R convertNcdfGds.R
        convertVcfGds.R BAFfromClusterMeans.R BAFfromGenotypes.R
        sdByScanChromWindow.R medianSdOverAutosomes.R
        meanSdByChromWindow.R findBAFvariance.R anomSegmentBAF.R
        anomFilterBAF.R anomDetectBAF.R LOHfind.R LOHselectAnoms.R
        anomDetectLOH.R anomSegStats.R anomStatsPlot.R
        anomIdentifyLowQuality.R alleleFrequency.R apartSnpSelection.R
        assocTestCPH.R assocTestFisherExact.R assocTestRegression.R
        batchChisqTest.R batchFisherTest.R chromIntensityPlot.R
        duplicateDiscordance.R duplicateDiscordanceAcrossDatasets.R
        duplicateDiscordanceProbability.R genoClusterPlot.R
        genoClusterPlotByBatch.R gwasExactHW.R hetByScanChrom.R
        hetBySnpSex.R intensityOutliersPlot.R manhattanPlot.R
        mendelErr.R meanIntensityByScanChrom.R
        missingGenotypeByScanChrom.R missingGenotypeBySnpSex.R
        pseudoautoIntensityPlot.R qqPlot.R qualityScoreByScan.R
        qualityScoreBySnp.R snpCorrelationPlot.R ibdAreasDraw.R
        ibdAssignRelatedness.R ibdPlot.R findRelationsMeanVar.R
        pedigreeCheck.R pedigreeDeleteDuplicates.R
        pedigreePairwiseRelatedness.R pedigreeMaxUnrelated.R
        simulateGenotypeMatrix.R simulateIntensityMatrix.R
Packaged: 2015-01-06 04:11:24 UTC; biocbuild
Built: R 3.1.2; ; 2015-01-06 15:19:57 UTC; windows
