Package: GWASTools
Version: 1.20.0
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, Sarah Nelson
Maintainer: Stephanie M. Gogarten <sdmorris@u.washington.edu>, Adrienne Stilp <amstilp@u.washington.edu>
Depends: Biobase
Imports: graphics, stats, utils, methods, ncdf4, gdsfmt, DBI, RSQLite,
        GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf,
        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-GdsReader.R
        Methods-GdsGenotypeReader.R Methods-GdsIntensityReader.R
        Methods-NcdfReader.R Methods-NcdfGenotypeReader.R
        Methods-NcdfIntensityReader.R Methods-MatrixGenotypeReader.R
        Methods-GenotypeData.R Methods-IntensityData.R
        createDataUtils.R createDataFile.R createAffyIntensityFile.R
        checkGenotypeFile.R checkIntensityFile.R setMissingGenotypes.R
        imputedDosageFile.R checkImputedDosageFile.R gdsSubset.R
        gdsSubsetCheck.R plinkUtils.R snpStats.R vcfWrite.R
        convertNcdfGds.R BAFfromClusterMeans.R BAFfromGenotypes.R
        genoClusterPlot.R genoClusterPlotByBatch.R chromIntensityPlot.R
        pseudoautoIntensityPlot.R intensityOutliersPlot.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
        hetByScanChrom.R hetBySnpSex.R missingGenotypeByScanChrom.R
        missingGenotypeBySnpSex.R meanIntensityByScanChrom.R
        qualityScoreByScan.R qualityScoreBySnp.R batchChisqTest.R
        batchFisherTest.R duplicateDiscordanceAcrossDatasets.R
        dupDosageCorAcrossDatasets.R duplicateDiscordance.R
        duplicateDiscordanceProbability.R assocRegression.R
        assocCoxPH.R exactHWE.R mendelErr.R qqPlot.R manhattanPlot.R
        snpCorrelationPlot.R ibdAreasDraw.R ibdAssignRelatedness.R
        ibdPlot.R findRelationsMeanVar.R pedigreeCheck.R
        pedigreeDeleteDuplicates.R pedigreePairwiseRelatedness.R
        pedigreeMaxUnrelated.R simulateGenotypeMatrix.R
        simulateIntensityMatrix.R defunct.R
NeedsCompilation: no
Packaged: 2016-10-17 23:21:51 UTC; biocbuild
Built: R 3.3.1; ; 2016-10-18 02:56:28 UTC; windows
