Package: GWASTools
Version: 1.55.0
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.
Authors@R: c(
  person("Stephanie M.", "Gogarten", role = "aut"),
  person("Cathy", "Laurie", role = "aut"),
  person("Tushar", "Bhangale", role = "aut"),
  person("Matthew P.", "Conomos", role = "aut"),
  person("Cecelia", "Laurie", role = "aut"),
  person("Michael", "Lawrence", role = "aut"),
  person("Caitlin", "McHugh", role = "aut"),
  person("Ian", "Painter", role = "aut"),
  person("Xiuwen", "Zheng", role = "aut"),
  person("Jess", "Shen", role = "aut"),
  person("Rohit", "Swarnkar", role = "aut"),
  person("Adrienne", "Stilp", role = "aut"),
  person("Sarah", "Nelson", role = "aut"),
  person("David", "Levine", role = "aut"),
  person("Sonali", "Kumari", role = "ctb",
    comment = "Converted vignettes from Sweave to RMarkdown / HTML."),
  person("Stephanie M.", "Gogarten",
    email = "sdmorris@uw.edu", role = "cre"))
Depends: Biobase
Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite,
        GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf,
        quantsmooth, data.table
Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings,
        GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors,
        VariantAnnotation, parallel, BiocStyle, knitr
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
VignetteBuilder: knitr
git_url: https://git.bioconductor.org/packages/GWASTools
git_branch: devel
git_last_commit: 88328f5
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-04 23:33:56 UTC; biocbuild
Author: Stephanie M. Gogarten [aut],
  Cathy Laurie [aut],
  Tushar Bhangale [aut],
  Matthew P. Conomos [aut],
  Cecelia Laurie [aut],
  Michael Lawrence [aut],
  Caitlin McHugh [aut],
  Ian Painter [aut],
  Xiuwen Zheng [aut],
  Jess Shen [aut],
  Rohit Swarnkar [aut],
  Adrienne Stilp [aut],
  Sarah Nelson [aut],
  David Levine [aut],
  Sonali Kumari [ctb] (Converted vignettes from Sweave to RMarkdown /
    HTML.),
  Stephanie M. Gogarten [cre]
Maintainer: Stephanie M. Gogarten <sdmorris@uw.edu>
Built: R 4.5.0; ; 2025-06-05 13:09:10 UTC; windows
