Package: GWASTools
Version: 1.10.1
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, sandwich
Imports: methods, DBI, RSQLite, GWASExactHW, DNAcopy, survival, 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-MatrixGenotypeReader.R Methods-GenotypeData.R
        Methods-IntensityData.R ncdfAddData.R ncdfAddIntensity.R
        ncdfCheckIntensity.R ncdfCheckGenotype.R ncdfCreate.R
        ncdfSubset.R ncdfSubsetCheck.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 ncdfSetMissingGenotypes.R
        gdsSetMissingGenotypes.R alleleFrequency.R apartSnpSelection.R
        assocTestCPH.R assocTestFisherExact.R assocTestRegression.R
        batchChisqTest.R batchFisherTest.R chromIntensityPlot.R
        duplicateDiscordance.R plinkUtils.R snpStats.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
        convertNcdfGds.R convertVcfGds.R ncdfImputedDosage.R
        simulateGenotypeMatrix.R simulateIntensityMatrix.R
        gdsImputedDosage.R gdsCheckImputedDosage.R gdsSubset.R
        gdsSubsetCheck.R
Packaged: 2014-04-23 09:53:34 UTC; biocbuild
Built: R 3.1.0; ; 2014-04-23 18:17:52 UTC; windows
