Functions to perform the following analyses: i) inferring epistasis from RNAi double knockdown data; ii) identifying gene pairs of multiple mutation patterns; iii) assessing association between gene pairs and survival; and iv) calculating the smallworldness of a graph (e.g., a gene interaction network). Data and analyses are described in Wang, X., Fu, A. Q., McNerney, M. and White, K. P. (2014). Widespread genetic epistasis among breast cancer genes. Nature Communications. 5 4828. <doi:10.1038/ncomms5828>.
Version: | 1.0.0 |
Depends: | R (≥ 2.10) |
Imports: | systemfit, qvalue, survival, reshape2, igraph |
Published: | 2016-04-01 |
Author: | Audrey Qiuyan Fu and Xiaoyue Wang |
Maintainer: | Audrey Q. Fu <audreyqyfu at gmail.com> |
License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
NeedsCompilation: | no |
CRAN checks: | cancerGI results |
Reference manual: | cancerGI.pdf |
Package source: | cancerGI_1.0.0.tar.gz |
Windows binaries: | r-devel: cancerGI_1.0.0.zip, r-release: cancerGI_1.0.0.zip, r-oldrel: cancerGI_1.0.0.zip |
OS X El Capitan binaries: | r-release: not available |
OS X Mavericks binaries: | r-oldrel: cancerGI_1.0.0.tgz |
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