AllelicImbalance

Package: AllelicImbalance
Type: Package
Title: Investigates allele specific expression
Version: 1.10.2
Date: 2016-04-02
Encoding: UTF-8
Author: Jesper R Gadin, Lasse Folkersen
Maintainer: Jesper R Gadin <j.r.gadin@gmail.com>
Description: Provides a framework for allelic specific expression
investigation using RNA-seq data.
License: GPL-3
URL: https://github.com/pappewaio/AllelicImbalance
BugReports: https://github.com/pappewaio/AllelicImbalance/issues
Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene,
SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown
Depends: R (>= 3.2.0), grid, GenomicRanges, SummarizedExperiment (>=
0.2.0), GenomicAlignments
Imports: methods, BiocGenerics, AnnotationDbi, BSgenome,
VariantAnnotation, Biostrings, S4Vectors (>= 0.9.25), IRanges,
Rsamtools, GenomicFeatures, Gviz, lattice, latticeExtra,
gridExtra, seqinr, GenomeInfoDb
LazyData: TRUE
biocViews: Genetics, Infrastructure, Sequencing
VignetteBuilder: knitr
Collate: 'AllelicImbalance-package.R' 'initialize-methods.R'
'ASEset-class.R' 'DetectedAI-class.R' 'GlobalAnalysis-class.R'
'barplot-methods.R' 'locationplot-methods.R'
'GvizTrack-methods.R' 'LinkVariantAlmlof-class.R'
'RegionSummary-class.R' 'RiskVariant-class.R'
'auxillary-functions-annotation.R'
'auxillary-functions-visuals.R'
'auxillary-methods-annotation.R'
'auxillary-methods-summaries.R' 'auxillary-methods.R'
'chisq.test-methods.R' 'binom.test-methods.R'
'boxplot-methods.R' 'deprecations.R' 'detect-methods.R'
'filter-methods.R' 'histplot-methods.R' 'inference-methods.R'
'linkage-methods.R' 'list-methods.R' 'mapbias-methods.R'
'plot-methods.R' 'show-methods.R' 'simulation-methods.R'
'summary-methods.R' 'utils.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 04:06:46 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'AllelicImbalance' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Creating a generic function for 'chisq.test' from package 'stats' in package 'AllelicImbalance'
Creating a generic function for 'binom.test' from package 'stats' in package 'AllelicImbalance'
Creating a generic function for 'hist' from package 'graphics' in package 'AllelicImbalance'
** help
*** installing help indices
  converting help for package 'AllelicImbalance'
    finding HTML links ... done
    ASEset-barplot                          html  
    ASEset-class                            html  
Rd warning: /tmp/Rtmpn6XHPp/R.INSTALL67335b663b45/AllelicImbalance/man/ASEset-class.Rd:168: missing file link 'RangedSummarizedExperiment'
Rd warning: /tmp/Rtmpn6XHPp/R.INSTALL67335b663b45/AllelicImbalance/man/ASEset-class.Rd:317: missing file link 'RangedSummarizedExperiment'
    ASEset-filters                          html  
    ASEset-gbarplot                         html  
    ASEset-glocationplot                    html  
    ASEset-gviztrack                        html  
    ASEset-scanForHeterozygotes             html  
    ASEset.old                              html  
    ASEset.sim                              html  
    ASEsetFromBam                           html  
    AllelicImbalance-package                html  
    DetectedAI-class                        html  
    DetectedAI-plot                         html  
    DetectedAI-summary                      html  
    GRvariants                              html  
    GlobalAnalysis-class                    html  
    LinkVariantAlmlof-class                 html  
    LinkVariantAlmlof-plot                  html  
    RegionSummary-class                     html  
    RiskVariant-class                       html  
    annotation-wrappers                     html  
    annotationBarplot                       html  
    barplot-lattice-support                 html  
    binom.test                              html  
    chisq.test                              html  
    cigar-utilities                         html  
Rd warning: /tmp/Rtmpn6XHPp/R.INSTALL67335b663b45/AllelicImbalance/man/cigar-utilities.Rd:56: missing file link 'GAlignmentsList'
    countAllelesFromBam                     html  
    coverageMatrixListFromGAL               html  
    decorateWithExons                       html  
    decorateWithGenes                       html  
    defaultMapBias                          html  
    defaultPhase                            html  
    detectAI                                html  
    fractionPlotDf                          html  
    gba                                     html  
    genomatrix                              html  
    genotype2phase                          html  
    getAlleleCounts                         html  
Rd warning: /tmp/Rtmpn6XHPp/R.INSTALL67335b663b45/AllelicImbalance/man/getAlleleCounts.Rd:80: missing file link 'GAlignmentsList'
    getAlleleQuality                        html  
    getAreaFromGeneNames                    html  
    getDefaultMapBiasExpMean                html  
    getSnpIdFromLocation                    html  
    histplot                                html  
    implodeList-old                         html  
    import-bam-2                            html  
    import-bam                              html  
    import-bcf                              html  
    inferAlleles                            html  
    inferAltAllele                          html  
    inferGenotypes                          html  
    initialize-ASEset                       html  
Rd warning: /tmp/Rtmpn6XHPp/R.INSTALL67335b663b45/AllelicImbalance/man/initialize-ASEset.Rd:127: missing file link 'RangedSummarizedExperiment'
    initialize-DetectedAI                   html  
    initialize-GlobalAnalysis               html  
    initialize-RiskVariant                  html  
    legendBarplot                           html  
    locationplot                            html  
    lva                                     html  
    lva.internal                            html  
    makeMaskedFasta                         html  
    mapBiasRef                              html  
    minCountFilt                            html  
    minFreqFilt                             html  
    multiAllelicFilt                        html  
    phase2genotype                          html  
    phaseArray2phaseMatrix                  html  
    phaseMatrix2Array                       html  
    randomRef                               html  
    reads                                   html  
    refAllele                               html  
    regionSummary                           html  
    scanForHeterozygotes-old                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AllelicImbalance)
Making 'packages.html' ... done