CNALR

CNALR is an R package to perform a stratification of tumour subtypes based on copy number alteration profiles using next-generation sequence data. This webpage is currently set to support the submission of the manuscript Stratifying tumour subtypes based on copy number alteration profiles using next-generation sequence data. The R package has currently been tested only in Linux/Unix environment. Download the R package here (version 1.0, 27 March 2014).

Data preparation

The input data for the CNALR package are basically the output of CNAnorm across different sequences/patients. After you normalise the CNA (per patient) using the CNAnorm package, save the results, preferably with .norm file extension.

Installing (and loading) the package

• If you have not had R installed, download and install R from the R project website (or directly from CRAN)

• Once you have downloaded the CNALR package, you can install it (from terminal)

  R CMD INSTALL CNALR_[version].tar.gz

  You can also install CNALR in your own directory by using

  R CMD INSTALL -l your-own-directory CNALR_[version].tar.gz

• Open R, and load the package by typing the following command in your R session

  library(CNALR)

  or

  library(CNALR, lib.loc="your-own-directory")

  if you have installed the package in your own directory (not in the default location).

• See the available functions and info by typing

  library(help=CNALR)

Last modified: Sat Apr 5 00:17:05 GMT 2014