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DESCRIPTION
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Package: GWASTools
Version: 1.33.3
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, David Levine
Maintainer: Stephanie M. Gogarten <[email protected]>
Depends: Biobase
Imports: graphics, stats, utils, methods, gdsfmt, DBI, RSQLite, GWASExactHW, DNAcopy, survival, sandwich, lmtest, logistf, quantsmooth, dplyr
Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation, parallel
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