Last data update: 2014.03.03


Package: aCGH
Title: Classes and functions for Array Comparative Genomic
Hybridization data.
Version: 1.50.0
Date: 2010-04-15
Depends: R (>= 2.10), cluster, survival, multtest
Imports: Biobase, cluster, grDevices, graphics, methods, multtest,
stats, survival, splines, utils
Author: Jane Fridlyand <>, Peter Dimitrov
Description: Functions for reading aCGH data from image analysis output
files and clone information files, creation of aCGH S3 objects
for storing these data. Basic methods for accessing/replacing,
subsetting, printing and plotting aCGH objects.
Maintainer: Peter Dimitrov <dimitrov@stat.Berkeley.EDU>
License: GPL-2
Collate: aCGH.R aCGH.plotting.R aCGH.test.R clusterGenome.R
funcs.dataplot.R heatmap.R hmm.R mergeLevels.R
LazyLoad: yes
biocViews: CopyNumberVariation, DataImport, Genetics
NeedsCompilation: yes
Packaged: 2016-05-04 02:42:00 UTC; biocbuild

● BiocViews: CopyNumberVariation, DataImport, Genetics
78 images, 26 functions, 3 datasets
Reverse Depends: 1

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'aCGH' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -g3 -I/usr/local/include    -fpic  -g -O2  -c hmm.cpp -o hmm.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o hmm.o -lm -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/aCGH/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'aCGH'
    finding HTML links ... done
    aCGH                                    html  
    aCGH.process                            html                        html  
    aCGH.test                               html  
    clusterGenome                           html  
    colorectal                              html  
    computeSD.func                          html  
    fga.func                                html                     html  
    find.hmm.states                         html  
    findAber.func                           html  
    findAmplif.func                         html  
    findOutliers.func                       html  
    findTrans.func                          html  
    gainLoss                                html  
    heatmap                                 html                  html                  html  
    impute.HMM                              html  
    impute.lowess                           html  
    mergeFunc                               html  
    mergeLevels                             html  
    plotFreqStat                            html  
    plotGenome                              html  
    plotHmmStates                           html  
    plotSummaryProfile                      html  
    states.hmm.func                         html  
    summarize.clones                        html  
    threshold.func                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Making 'packages.html' ... done