Analyses of Cancer Gene Interaction
Compute smallworldness of a graph
Survival analysis for pairs of genes
Survival analysis for pairs of genes (with matched individuals)
Write results from survival analysis to output for one pair of genes
Survival analysis for one pair of genes
Generate a design matrix from raw RNAi data.
Find matched individuals in mutation and survival data
Compute the p and q values of all pairwise gene mutation patterns
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>.