GWASTools

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

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'GWASTools' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'open' from package 'base' in package 'GWASTools'
Creating a generic function for 'close' from package 'base' in package 'GWASTools'
** help
*** installing help indices
  converting help for package 'GWASTools'
    finding HTML links ... done
    BAFfromClusterMeans                     html  
    finding level-2 HTML links ... done

    BAFfromGenotypes                        html  
    GWASTools-package                       html  
    GdsGenotypeReader-class                 html  
    GdsIntensityReader-class                html  
    GdsReader-class                         html  
    GenotypeData-class                      html  
    HLA                                     html  
    IntensityData-class                     html  
    MatrixGenotypeReader-class              html  
    NcdfGenotypeReader-class                html  
    NcdfIntensityReader-class               html  
    NcdfReader-class                        html  
    ScanAnnotationDataFrame-class           html  
    ScanAnnotationSQLite-class              html  
    SnpAnnotationDataFrame-class            html  
    SnpAnnotationSQLite-class               html  
    alleleFrequency                         html  
    allequal                                html  
    anomDetectBAF                           html  
    anomDetectLOH                           html  
    anomIdentifyLowQuality                  html  
    anomSegStats                            html  
    apartSnpSelection                       html  
    assocCoxPH                              html  
    assocRegression                         html  
    batchTest                               html  
    centromeres                             html  
    chromIntensityPlot                      html  
    convertNcdfGds                          html  
Rd warning: /tmp/RtmpoWRnE6/R.INSTALL54173cebfa15/GWASTools/man/convertNcdfGds.Rd:66: missing file link 'gdsfmt'
    convertVcfGds                           html  
    createDataFile                          html  
    defunct                                 html  
    deprecated                              html  
    duplicateDiscordance                    html  
    duplicateDiscordanceAcrossDatasets      html  
    duplicateDiscordanceProbability         html  
    exactHWE                                html  
    findBAFvariance                         html  
    gdsSubset                               html  
    genoClusterPlot                         html  
    genotypeToCharacter                     html  
    getVariable                             html  
    getobj                                  html  
    hetByScanChrom                          html  
    hetBySnpSex                             html  
    ibdPlot                                 html  
    imputedDosageFile                       html  
    intensityOutliersPlot                   html  
    manhattanPlot                           html  
    meanIntensityByScanChrom                html  
    mendelErr                               html  
    mendelList                              html  
    missingGenotypeByScanChrom              html  
    missingGenotypeBySnpSex                 html  
    pasteSorted                             html  
    pcaSnpFilters                           html  
    pedigreeCheck                           html  
    pedigreeDeleteDuplicates                html  
    pedigreeMaxUnrelated                    html  
    pedigreePairwiseRelatedness             html  
    plinkToNcdf                             html  
    plinkUtils                              html  
    pseudoautoIntensityPlot                 html  
    pseudoautosomal                         html  
    qqPlot                                  html  
    qualityScoreByScan                      html  
    qualityScoreBySnp                       html  
    readWriteFirst                          html  
    relationsMeanVar                        html  
    saveas                                  html  
    setMissingGenotypes                     html  
    simulateGenotypeMatrix                  html  
    snpCorrelationPlot                      html  
    snpStats                                html  
    vcfWrite                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GWASTools)
Making 'packages.html' ... done