cancerGI: Analyses of Cancer Gene Interaction

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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>.

Author
Audrey Qiuyan Fu and Xiaoyue Wang
Date of publication
2016-04-01 16:42:25
Maintainer
Audrey Q. Fu <audreyqyfu@gmail.com>
License
GPL (>= 2)
Version
1.0.0

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Man pages

cancerGI-package
Statistical Analyses of Genetic Interactions in Cancer
computeSmallWorldness
Compute smallworldness of a graph
computeSurvivalPValueForGenePairSet.output
Survival analysis for pairs of genes
computeSurvivalPValueGenePairAll.output
Survival analysis for pairs of genes (with matched...
computeSurvivalPValueOneGenePair
Survival analysis for one pair of genes
computeSurvivalPValueOneGenePair.output
Write results from survival analysis to output for one pair...
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...
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...

Files in this package

cancerGI
cancerGI/NAMESPACE
cancerGI/data
cancerGI/data/tested_pairs.rda
cancerGI/data/survival.rda
cancerGI/data/RNAi.rda
cancerGI/data/mutations.rda
cancerGI/R
cancerGI/R/testMutationalPatternAll.R
cancerGI/R/processDataMutSurv.R
cancerGI/R/computeSurvivalPValueOneGenePair.output.R
cancerGI/R/computeSurvivalPValueForGenePairSet.output.R
cancerGI/R/testMutationalPatternPair.R
cancerGI/R/computeSurvivalPValueGenePairAll.output.R
cancerGI/R/constructDesignMatrix.R
cancerGI/R/testMutationalPatternAll.wrapper.R
cancerGI/R/findSurvMedian.R
cancerGI/R/computeSmallWorldness.R
cancerGI/R/computeSurvivalPValueOneGenePair.R
cancerGI/R/testMutationalPatternBinom.R
cancerGI/R/computeSurvivalPValueGenePairAll.R
cancerGI/MD5
cancerGI/DESCRIPTION
cancerGI/man
cancerGI/man/testMutationalPatternAll.wrapper.Rd
cancerGI/man/computeSurvivalPValueOneGenePair.output.Rd
cancerGI/man/cancerGI-package.Rd
cancerGI/man/processDataMutSurv.Rd
cancerGI/man/survival.Rd
cancerGI/man/computeSurvivalPValueForGenePairSet.output.Rd
cancerGI/man/mutations.Rd
cancerGI/man/computeSmallWorldness.Rd
cancerGI/man/computeSurvivalPValueGenePairAll.output.Rd
cancerGI/man/constructDesignMatrix.Rd
cancerGI/man/RNAi.Rd
cancerGI/man/computeSurvivalPValueOneGenePair.Rd
cancerGI/man/tested_pairs.Rd