Installation

Rawcopy dependencies:

R:

Rawcopy is an R-package, download and install the development version of R (r-base-dev) from:
https://cran.r-project.org/

R-code from Bioconductor:

source("http://bioconductor.org/biocLite.R")
biocLite("affxparser")
biocLite("DNAcopy")
biocLite("aroma.light")

If biocLite doesn’t work, the Package Source files have to be downloaded and installed manually from:

http://www.bioconductor.org/packages/release/bioc/html/affxparser.html
http://www.bioconductor.org/packages/release/bioc/html/DNAcopy.html

install.packages('Path/affxparser_1.38.0.tar.gz',type='source',repos=NULL)
install.packages('Path/DNAcopy_1.40.0.tar.gz',type='source',repos=NULL)

R-code from cran:

install.packages(c('foreach','doMC','PSCBS','squash','digest','ape','SDMTools'))

If PSCBS doesn’t work, the package source files have to be downloaded and installed manually from:
https://cran.r-project.org/src/contrib/Archive/PSCBS/PSCBS_0.43.0.tar.gz

install.packages(c('R.utils','matrixStats','R.cache'))
install.packages('Path/PSCBS_0.43.0.tar.gz',repos=NULL,type='source')

Rawcopy installation:

install.packages('rawcopy',repos='http://array.medsci.uu.se/R',type='source')

When running on windows you may get these warnings messages:

  1. package ‘foreach’ was built under R version 3.1.2
  2. package ‘PSCBS’ was built under R version 3.1.2
  3. executing %dopar% sequentially: no parallel backend registered

Source code:

The source code is available on bitbucket:
https://bitbucket.org/n0s3n/rawcopy

Older versions:

Older versions of Rawcopy are available at
http://array.medsci.uu.se/R/src/contrib/