deepSNV

Package: deepSNV
Maintainer: Moritz Gerstung <mg14@sanger.ac.uk>
License: GPL-3
Title: Detection of subclonal SNVs in deep sequencing data.
biocViews: GeneticVariability, SNP, Sequencing, Genetics, DataImport
LinkingTo: Rhtslib
Type: Package
LazyLoad: yes
Authors@R: c( person("Niko","Beerenwinkel", role="ths"),
person("David", "Jones", role = "ctb"),
person("Inigo", "Martincorena", role = "ctb"),
person("Moritz","Gerstung",
email = "mg14@sanger.ac.uk", role= c("aut","cre")) )
Description: This package provides provides quantitative variant callers for
detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing
experiments. The deepSNV algorithm is used for a comparative setup with a
control experiment of the same loci and uses a beta-binomial model and a
likelihood ratio test to discriminate sequencing errors and subclonal SNVs.
The shearwater algorithm computes a Bayes classifier based on a
beta-binomial model for variant calling with multiple samples for
precisely estimating model parameters such as local error rates and
dispersion and prior knowledge, e.g. from variation data bases such as
COSMIC.
Version: 1.18.1
URL: http://github.com/mg14/deepSNV
Depends: R (>= 2.13.0), methods, graphics, parallel, Rhtslib, IRanges,
GenomicRanges, SummarizedExperiment, Biostrings, VGAM,
VariantAnnotation (>= 1.13.44),
Imports: Rhtslib
Suggests: RColorBrewer, knitr
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-05-12 03:17:01 UTC; biocbuild
Author: Niko Beerenwinkel [ths],
David Jones [ctb],
Inigo Martincorena [ctb],
Moritz Gerstung [aut, cre]

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'deepSNV' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking malloc.h usability... yes
checking malloc.h presence... yes
checking for malloc.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
checking for stddef.h... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for _LARGEFILE_SOURCE value needed for large files... no
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for working memcmp... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for off_t... yes
checking for size_t... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include"   -fpic  -g -O2  -c bam2R.cpp -o bam2R.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rhtslib/include"   -fpic  -g -O2  -c betabinom.c -o betabinom.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o deepSNV.so bam2R.o betabinom.o -L/home/ddbj/local/lib64/R/library/Rhtslib/lib -Wl,-rpath,/home/ddbj/local/lib64/R/library/Rhtslib/lib -lhts -lz -pthread -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/deepSNV/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'deepSNV'
    finding HTML links ... done
    Extract-methods                         html  
    RCC                                     html  
    RF                                      html  
    bam2R                                   html  
    betabinLRT                              html  
    bf2Vcf                                  html  
    finding level-2 HTML links ... done

    consensusSequence-methods               html  
    control-methods                         html  
    coordinates-methods                     html  
    counts                                  html  
    dbetabinom                              html  
    deepSNV-class                           html  
    deepSNV-methods                         html  
    deepSNV-package                         html  
    estimateDirichlet-methods               html  
    estimateDispersion-methods              html  
    estimateRho                             html  
    loadAllData                             html  
    makePrior                               html  
    manhattanPlot                           html  
    mcChunk                                 html  
    normalize-methods                       html  
    p.combine                               html  
    p.val-methods                           html  
    pbetabinom                              html  
    phiX                                    html  
    pi                                      html  
    plot.deepSNV                            html  
    qvals2Vcf                               html  
    repeatMask-methods                      html  
    shearwater                              html  
    show-deepSNV-method                     html  
    summary-methods                         html  
    test-methods                            html  
    trueSNVs                                html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (deepSNV)
Making 'packages.html' ... done