Analyses of Cancer Gene Interaction

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Documentation for package ‘cancerGI’ version 1.0.1

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computeSmallWorldness Compute smallworldness of a graph
computeSurvivalPValueForGenePairSet.output Survival analysis for pairs of genes
computeSurvivalPValueGenePairAll.output Survival analysis for pairs of genes (with matched individuals)
computeSurvivalPValueOneGenePair Survival analysis for one pair of genes
computeSurvivalPValueOneGenePair.output Write results from survival analysis to output for one pair of genes
constructDesignMatrix Generate a design matrix from raw RNAi data.
mutations Genetic mutation data in patients.
processDataMutSurv Find matched individuals in mutation and survival data
RNAi Molecular phenotypes from single and double knockdowns in RNAi screen
survival Patient survival data.
tested_pairs Gene pairs tested in the double knockdown assay.
testMutationalPatternAll.wrapper Compute the p and q values of all pairwise gene mutation patterns