methyAnalysis

Package: methyAnalysis
Type: Package
Title: DNA methylation data analysis and visualization
Version: 1.14.0
Date: 2016-03-15
Depends: R (>= 2.10), grid, BiocGenerics, IRanges, GenomeInfoDb,
GenomicRanges, Biobase (>= 2.5.5), org.Hs.eg.db
Imports: lumi, methylumi, Gviz, genoset, SummarizedExperiment,
GenomicRanges, VariantAnnotation, IRanges, rtracklayer,
GenomicFeatures, annotate, Biobase (>= 2.5.5), AnnotationDbi,
genefilter, biomaRt, methods, parallel
Suggests: FDb.InfiniumMethylation.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene
Author: Pan Du, Richard Bourgon
Maintainer: Pan Du <dupan.mail@gmail.com>
Description: The methyAnalysis package aims for the DNA methylation data
analysis and visualization. A MethyGenoSet class is defined to keep the
chromosome location information together with the data. The package also includes
functions of estimating the methylation levels from Methy-Seq data.
License: Artistic-2.0
LazyLoad: yes
biocViews: Microarray, DNAMethylation, Visualization
Collate: 'MethyGenoSet-class.R' 'methyAnalysis.R'
'heatmapByChromosome.R' 'methyl-seq.R'
NeedsCompilation: no
Packaged: 2016-05-04 04:43:50 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'methyAnalysis' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: multiple methods tables found for 'colMeans'
Warning: multiple methods tables found for 'colSums'
Warning: multiple methods tables found for 'rowMeans'
Warning: multiple methods tables found for 'rowSums'
No methods found in "GenomicRanges" for requests: overlapsAny
No methods found in "genoset" for requests: rowRanges, rowRanges<-, toGenomeOrder
** help
*** installing help indices
  converting help for package 'methyAnalysis'
    finding HTML links ... done
    MethyGenoSet-class                      html  
    finding level-2 HTML links ... done

Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:34: missing file link 'GenoSet'
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:36: missing file link 'GenoSet'
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:46: missing file link 'GenoSet'
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:51: missing file link 'SummarizedExperiment'
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:57: missing file link 'SummarizedExperiment'
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:58: missing file link 'colData'
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:86: missing file link 'GenoSet'
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:91: missing file link 'SummarizedExperiment'
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:92: missing file link 'GenoSet'
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:92: missing file link 'SummarizedExperiment'
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:100: missing file link 'GenoSet'
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/MethyGenoSet-class.Rd:100: missing file link 'SummarizedExperiment'
    MethyLumiM2GenoSet                      html  
    annotateDMRInfo                         html  
    annotateGRanges                         html  
    asBigMatrix-methods                     html  
Rd warning: /tmp/Rtmpb1DWYf/R.INSTALL503e621aadd1/methyAnalysis/man/asBigMatrix-methods.Rd:15: missing file link 'GenoSet'
    buildAnnotationTracks                   html  
    checkChrName                            html  
    createTranscriptTrack                   html  
    detectDMR.slideWin                      html  
    estimateCMR.methylation                 html  
    estimateMethySeq                        html  
    exampleMethyGenoSet                     html  
    export.DMRInfo                          html  
    export.methyGenoSet                     html  
    filterBisulfiteVariant                  html  
    getContinuousRegion                     html  
    getCoverage                             html  
    heatmapByChromosome                     html  
    identifyCpG                             html  
    identifySigDMR                          html  
    plotHeatmapByGene                       html  
    plotMethylationHeatmapByGene            html  
    plotTracksWithDataTrackInfo             html  
    smoothMethyData                         html  
    updateMethyGenoSet                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: multiple methods tables found for 'colMeans'
Warning: multiple methods tables found for 'colSums'
Warning: multiple methods tables found for 'rowMeans'
Warning: multiple methods tables found for 'rowSums'
No methods found in "GenomicRanges" for requests: overlapsAny
No methods found in "genoset" for requests: rowRanges, rowRanges<-, toGenomeOrder
* DONE (methyAnalysis)
Making 'packages.html' ... done