MinimumDistance

Package: MinimumDistance
Title: A Package for De Novo CNV Detection in Case-Parent Trios
Version: 1.16.0
Date: 2016-03-05
Author: Robert B Scharpf and Ingo Ruczinski
Maintainer: Robert B Scharpf <rscharpf@jhu.edu>
Description: Analysis of de novo copy number variants in trios from
high-dimensional genotyping platforms.
License: Artistic-2.0
Depends: R (>= 3.0.1), VanillaICE (>= 1.31.3)
Imports: methods, BiocGenerics, Biobase, S4Vectors (>= 0.9.25),
IRanges, GenomeInfoDb, GenomicRanges (>= 1.17.16),
SummarizedExperiment (>= 0.2.0), oligoClasses, DNAcopy, ff,
foreach, matrixStats, lattice, data.table, grid, stats, utils
Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18,
BSgenome.Hsapiens.UCSC.hg19, SNPchip, RUnit
Collate: 'help.R' 'AllClasses.R' 'AllGenerics.R' 'coercion-methods.R'
'datasets.R' 'defunct.R' 'functions.R' 'generator-funs.R'
'lattice-methods.R' 'mad-methods.R'
'methods-AnnotatedDataFrame.R' 'methods-AssayData.R'
'methods-FileViews.R' 'methods-FilterParamMD.R'
'methods-ILimit.R' 'methods-MDRanges.R'
'methods-MinDistExperiment.R' 'methods-MinDistGRanges.R'
'methods-MinDistParam.R' 'methods-MinDistPosterior.R'
'methods-ParentOffspring.R' 'methods-ParentOffspringList.R'
'methods-Pedigree.R' 'methods-PennParam.R'
'methods-ShallowSimpleList.R' 'methods-SummarizedExperiment.R'
'methods-TrioSet.R' 'methods-TrioSetList.R'
'methods-ff_array.R' 'methods-grid.R' 'methods-list.R'
'methods-matrix.R' 'segment2-methods.R' 'utils.R' 'zzz.R'
Enhances: snow, doSNOW
LazyLoad: yes
biocViews: Microarray, SNP, CopyNumberVariation
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-04 04:31:04 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MinimumDistance' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'allNames' in package 'MinimumDistance'
Creating a generic function for 'colMads' from package 'matrixStats' in package 'MinimumDistance'
** help
*** installing help indices
  converting help for package 'MinimumDistance'
    finding HTML links ... done
    DNAcopyParam                            html  
    Defunct                                 html  
    Deprecated                              html  
    FilterParamMD-class                     html  
    FilterParamMD                           html  
Rd warning: /tmp/RtmpojGQZU/R.INSTALL6126da93188/MinimumDistance/man/FilterParamMD.Rd:14: missing file link 'FilterParam'
    MAP                                     html  
    MAP2                                    html  
    MDRanges-class                          html  
    MinDistExperiment-class                 html  
    MinDistExperiment                       html  
    MinDistGRanges-class                    html  
    MinDistGRanges                          html  
    MinDistParam-class                      html  
    MinDistParam                            html  
    MinDistPosterior-class                  html  
    MinimumDistance                         html  
    ParentOffspring-class                   html  
    ParentOffspringList-class               html  
    Pedigree-class                          html  
    Pedigree                                html  
    PennParam                               html  
    TrioSet-class                           html  
    TrioSet                                 html  
    TrioSetList-class                       html  
    TrioSetList                             html  
    TrioSetListLD                           html  
    acf2                                    html  
    calculateMindist                        html  
    coercion-methods                        html  
    denovo                                  html  
    exampleTrioSetList                      html  
    filterExperiment                        html  
    mad2                                    html  
    mdLegend                                html  
    md_exp                                  html  
    md_gr                                   html  
    mindist                                 html  
    nMAD                                    html  
    pedigreeGrid                            html  
    pedigreeName                            html  
    pedigreeViewports                       html  
    plotDenovo                              html  
    range-ILimit-method                     html  
    segment2                                html  
    finding level-2 HTML links ... done

** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MinimumDistance)
Making 'packages.html' ... done