cn.mops

Package: cn.mops
Maintainer: Guenter Klambauer <cn.mops@bioinf.jku.at>
Author: Guenter Klambauer
License: LGPL (>= 2.0)
Type: Package
Title: cn.mops - Mixture of Poissons for CNV detection in NGS data
Description: cn.mops (Copy Number estimation by a Mixture Of PoissonS)
is a data processing pipeline for copy number variations and
aberrations (CNVs and CNAs) from next generation sequencing
(NGS) data. The package supplies functions to convert BAM files
into read count matrices or genomic ranges objects, which are
the input objects for cn.mops. cn.mops models the depths of
coverage across samples at each genomic position. Therefore, it
does not suffer from read count biases along chromosomes. Using
a Bayesian approach, cn.mops decomposes read variations across
samples into integer copy numbers and noise by its mixture
components and Poisson distributions, respectively. cn.mops
guarantees a low FDR because wrong detections are indicated by
high noise and filtered out. cn.mops is very fast and written
in C++.
Version: 1.18.0
Date: 2016-03-03
URL: http://www.bioinf.jku.at/software/cnmops/cnmops.html
Depends: R (>= 2.12), methods, utils, stats, graphics, parallel,
GenomicRanges
Imports: BiocGenerics, Biobase, IRanges, Rsamtools, GenomeInfoDb,
S4Vectors
Suggests: DNAcopy
LazyLoad: yes
biocViews: Sequencing, CopyNumberVariation, Homo_sapiens, CellBiology,
HapMap, Genetics
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-05-04 04:18:46 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'cn.mops' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c R_init_cnmops.c -o R_init_cnmops.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cnmops.cpp -o cnmops.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c segment.cpp -o segment.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o cn.mops.so R_init_cnmops.o cnmops.o segment.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/cn.mops/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'cn.mops'
    finding HTML links ... done
    CNVDetectionResult                      html  
    CNVRanges                               html  
    X                                       html  
    XRanges                                 html  
    calcFractionalCopyNumbers-CNVDetectionResult-method
                                            html  
    calcFractionalCopyNumbers               html  
    calcIntegerCopyNumbers-CNVDetectionResult-method
                                            html  
    calcIntegerCopyNumbers                  html  
    cn.mops                                 html  
    cnvr-CNVDetectionResult-method          html  
    cnvr                                    html  
    cnvs-CNVDetectionResult-method          html  
    cnvs                                    html  
    exomeCounts                             html  
    exomecn.mops                            html  
    getReadCountsFromBAM                    html  
    getSegmentReadCountsFromBAM             html  
    gr-CNVDetectionResult-method            html  
    gr                                      html  
    haplocn.mops                            html  
    individualCall-CNVDetectionResult-method
                                            html  
    individualCall                          html  
    iniCall-CNVDetectionResult-method       html  
    iniCall                                 html  
    integerCopyNumber-CNVDetectionResult-method
                                            html  
    integerCopyNumber                       html  
    localAssessments-CNVDetectionResult-method
                                            html  
    localAssessments                        html  
    makeRobustCNVR                          html  
    normalizeChromosomes                    html  
    normalizeGenome                         html  
    normalizedData-CNVDetectionResult-method
                                            html  
    normalizedData                          html  
    params-CNVDetectionResult-method        html  
    params                                  html  
    plot                                    html  
    posteriorProbs-CNVDetectionResult-method
                                            html  
    posteriorProbs                          html  
    referencecn.mops                        html  
    sampleNames-CNVDetectionResult-method   html  
    sampleNames                             html  
    segment                                 html  
    segmentation-CNVDetectionResult-method
                                            html  
    segmentation                            html  
    segplot-CNVDetectionResult-method       html  
    segplot                                 html  
    show                                    html  
    singlecn.mops                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.mops)
Making 'packages.html' ... done