Package: GWASTools
Version: 1.30.1
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, Michael Lawrence, Caitlin McHugh, Ian Painter, Xiuwen Zheng, Jess Shen, Rohit Swarnkar, Adrienne Stilp, Sarah Nelson
Maintainer: Stephanie M. Gogarten <sdmorris@uw.edu>
Depends: Biobase
Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite,
        GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf,
        quantsmooth
Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings,
        GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors,
        VariantAnnotation
License: Artistic-2.0
URL: https://github.com/smgogarten/GWASTools
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
        Methods-Iterator.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 asVCF.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
git_url: https://git.bioconductor.org/packages/GWASTools
git_branch: RELEASE_3_9
git_last_commit: ea23223
git_last_commit_date: 2019-10-07
Date/Publication: 2019-10-10
NeedsCompilation: no
Packaged: 2019-10-11 02:02:40 UTC; biocbuild
Built: R 3.6.1; ; 2019-10-11 13:10:57 UTC; windows
