Package: GWASTools
Version: 1.14.2
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, Sarah Nelson
Maintainer: Stephanie M. Gogarten <sdmorris@u.washington.edu>, Adrienne Stilp <amstilp@u.washington.edu>
Depends: Biobase
Imports: methods, ncdf, 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 createDataFile.R
        createAffyIntensityFile.R checkGenotypeFile.R
        checkIntensityFile.R setMissingGenotypes.R imputedDosageFile.R
        checkImputedDosageFile.R ncdfSubset.R ncdfSubsetCheck.R
        gdsSubset.R gdsSubsetCheck.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
        hetByScanChrom.R hetBySnpSex.R missingGenotypeByScanChrom.R
        missingGenotypeBySnpSex.R meanIntensityByScanChrom.R
        qualityScoreByScan.R qualityScoreBySnp.R batchChisqTest.R
        batchFisherTest.R duplicateDiscordance.R
        duplicateDiscordanceProbability.R
        duplicateDiscordanceAcrossDatasets.R
        dupDosageCorAcrossDatasets.R assocRegression.R assocCoxPH.R
        exactHWE.R mendelErr.R genoClusterPlot.R
        genoClusterPlotByBatch.R chromIntensityPlot.R
        pseudoautoIntensityPlot.R intensityOutliersPlot.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
        assocTestCPH.R assocTestFisherExact.R assocTestRegression.R
        gwasExactHW.R
NeedsCompilation: no
Packaged: 2015-10-08 03:52:45 UTC; biocbuild
Built: R 3.2.2; ; 2015-10-08 09:50:21 UTC; windows
