exomeCopy

Package: exomeCopy
Type: Package
Title: Copy number variant detection from exome sequencing read depth
Version: 1.18.0
Date: 2016-02-11
Author: Michael Love
Maintainer: Michael Love <michaelisaiahlove@gmail.com>
Description: Detection of copy number variants (CNV) from exome
sequencing samples, including unpaired samples. The package
implements a hidden Markov model which uses positional
covariates, such as background read depth and GC-content, to
simultaneously normalize and segment the samples into regions
of constant copy count.
License: GPL (>= 2)
LazyLoad: yes
Imports: stats4, methods, GenomeInfoDb
Depends: IRanges (>= 2.5.27), GenomicRanges (>= 1.23.16), Rsamtools
Suggests: Biostrings
biocViews: CopyNumberVariation, Sequencing, Genetics
NeedsCompilation: yes
Packaged: 2016-05-04 04:18:09 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'exomeCopy' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c exomeCopy.c -o exomeCopy.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o exomeCopy.so exomeCopy.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/exomeCopy/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'exomeCopy'
    finding HTML links ... done
    ExomeCopy-class                         html  
    compileCopyCountSegments                html  
    copyCountSegments                       html  
    countBamInGRanges                       html  
    finding level-2 HTML links ... done

    exomeCopy-package                       html  
    exomeCopy                               html  
    exomecounts                             html  
    generateBackground                      html  
    getGCcontent                            html  
    negLogLike                              html  
    plot.exomeCopyObject                    html  
    plotCompiledCNV                         html  
    subdivideGRanges                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (exomeCopy)
Making 'packages.html' ... done