我的操作系统：Ubuntu 16.04 LTS
GISTIC2.0用以分析癌症拷贝数变异的一个数据处理模块。具体介绍如下——
Summary:
The GISTIC module identifies regions of the genome that are significantly amplified or deleted across a set of samples. Each aberration is assigned a G-score that considers the amplitude of the aberration as well as the frequency of its occurrence across samples. False Discovery Rate q-values are then calculated for the aberrant regions, and regions with q-values below a user-defined threshold are considered significant. For each significant region, a “peak region” is identified, which is the part of the aberrant region with greatest amplitude and frequency of alteration. In addition, a “wide peak” is determined using a leave-one-out algorithm to allow for errors in the boundaries in a single sample. The “wide peak” boundaries are more robust for identifying the most likely gene targets in the region. Each significantly aberrant region is also tested to determine whether it results primarily from broad events (longer than half a chromosome arm), focal events, or significant levels of both. The GISTIC module reports the genomic locations and calculated q-values for the aberrant regions. It identifies the samples that exhibit each significant amplification or deletion, and it lists genes found in each “wide peak” region.
References:
Mermel C, Schumacher S, et al. (2011). "GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers." Genome Biology, 12:R41.
Beroukhim R, Mermel C, et al. (2010). "The landscape of somatic copy -number alteration across human cancers." Nature, 463:899-905.
· Beroukhim R, Getz G, et al. (2007). “Assessing the significance of chromosomal abberations in cancer: Methodology and application to glioma.” Proc Natl Acad Sci, 104:20007-20012.
虽然别人已经把软件做好了，但是刚开始使用，还是会遇到诸多问题，因此我记录一下我的一些经验。
模块的下载与安装
FILL IN <mcr_root> HERE #####set mcr_root = <mcr_root> $thisdir/MATLAB_Component_Runtimeset mcr_root = /home/wsx/GISTIC2.0 $thisdir/MATLAB_Component_Runtimesetenv LD_LIBRARY_PATH $mcr_root/v714/runtime/glnxa64:$LD_LIBRARY_PATHsetenv LD_LIBRARY_PATH $mcr_root/v714/sys/os/glnxa64:$LD_LIBRARY_PATHsetenv LD_LIBRARY_PATH $mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:$LD_LIBRARY_PATHsetenv LD_LIBRARY_PATH $mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:$LD_LIBRARY_PATHsetenv LD_LIBRARY_PATH $mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64:$LD_LIBRARY_PATHsetenv XAPPLRESDIR $mcr_root/v714/X11/app-defaults#####################################
如果你的系统与我一样是Ubuntu，或者是使用的bash命令，可以在 ~/.bashrc文件添加下列脚本：
export mcr_root=/home/wsx/GISTIC2.0/MATLAB_Component_Runtimeexport LD_LIBRARY_PATH=$mcr_root/v714/runtime/glnxa64:$LD_LIBRARY_PATHexport LD_LIBRARY_PATH=$mcr_root/v714/sys/os/glnxa64:$LD_LIBRARY_PATHexport LD_LIBRARY_PATH=$mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:$LD_LIBRARY_PATHexport LD_LIBRARY_PATH=$mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64/server:$LD_LIBRARY_PATHexport LD_LIBRARY_PATH=$mcr_root/v714/sys/java/jre/glnxa64/jre/lib/amd64:$LD_LIBRARY_PATHexport XAPPLRESDIR=$mcr_root/v714/X11/app-defaults
注销重进，用export命令或者env命令查看环境变量是否添加成功。
最后，我们就可以看到示例文件运行的结果，各种生成的图片晃过眼睛，然后保存在(GISTIC2.0)安装目录的example_results文件夹下。