cancerGI: Analyses of Cancer Gene Interaction
Version 1.0.0

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. .

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AuthorAudrey Qiuyan Fu and Xiaoyue Wang
Date of publication2016-04-01 16:42:25
MaintainerAudrey Q. Fu <audreyqyfu@gmail.com>
LicenseGPL (>= 2)
Version1.0.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("cancerGI")

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...

Functions

RNAi Man page
cancerGI Man page
cancerGI-package Man page
computeSmallWorldness Man page Source code
computeSurvivalPValueForGenePairSet.output Man page Source code
computeSurvivalPValueGenePairAll Source code
computeSurvivalPValueGenePairAll.output Man page Source code
computeSurvivalPValueOneGenePair Man page Source code
computeSurvivalPValueOneGenePair.output Man page Source code
constructDesignMatrix Man page Source code
findSurvMedian Source code
mutations Man page
processDataMutSurv Man page Source code
survival Man page
testMutationalPatternAll Source code
testMutationalPatternAll.wrapper Man page Source code
testMutationalPatternBinom Source code
testMutationalPatternPair Source code
tested_pairs Man page

Files

NAMESPACE
data
data/tested_pairs.rda
data/survival.rda
data/RNAi.rda
data/mutations.rda
R
R/testMutationalPatternAll.R
R/processDataMutSurv.R
R/computeSurvivalPValueOneGenePair.output.R
R/computeSurvivalPValueForGenePairSet.output.R
R/testMutationalPatternPair.R
R/computeSurvivalPValueGenePairAll.output.R
R/constructDesignMatrix.R
R/testMutationalPatternAll.wrapper.R
R/findSurvMedian.R
R/computeSmallWorldness.R
R/computeSurvivalPValueOneGenePair.R
R/testMutationalPatternBinom.R
R/computeSurvivalPValueGenePairAll.R
MD5
DESCRIPTION
man
man/testMutationalPatternAll.wrapper.Rd
man/computeSurvivalPValueOneGenePair.output.Rd
man/cancerGI-package.Rd
man/processDataMutSurv.Rd
man/survival.Rd
man/computeSurvivalPValueForGenePairSet.output.Rd
man/mutations.Rd
man/computeSmallWorldness.Rd
man/computeSurvivalPValueGenePairAll.output.Rd
man/constructDesignMatrix.Rd
man/RNAi.Rd
man/computeSurvivalPValueOneGenePair.Rd
man/tested_pairs.Rd
cancerGI documentation built on May 19, 2017, 2:13 p.m.