Package: GWASTools
Version: 1.49.0
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