Package: GWASTools
Version: 1.18.0
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.
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, ncdf4, 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
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
convertNcdfGds.R convertVcfGds.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 duplicateDiscordance.R
duplicateDiscordanceProbability.R
duplicateDiscordanceAcrossDatasets.R
dupDosageCorAcrossDatasets.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 defunct.R
NeedsCompilation: no
Packaged: 2016-05-04 04:15:23 UTC; biocbuild
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