CancerMutationAnalysis: Cancer mutation analysis

This package implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver genes (which play an active role in tumorigenesis) and passenger genes (which are mutated in tumor samples, but have no role in tumorigenesis) and incorporate a two-stage study design. The gene-set methods implement a patient-oriented approach, which calculates gene-set scores for each sample, then combines them across samples; a gene-oriented approach which uses the Wilcoxon test is also provided for comparison.

AuthorGiovanni Parmigiani, Simina M. Boca
Date of publicationNone
MaintainerSimina M. Boca <smb310@georgetown.edu>
LicenseGPL (>= 2) + file LICENSE
Version1.16.0

View on Bioconductor

Man pages

BackRatesBreast: Data from the Wood et al. 2007 study: Background mutation...

BackRatesColon: Data from the Wood et al. 2007 study: Background mutation...

BackRatesGBM: Data from the Parsons et al. 2008 study: Background mutation...

BackRatesMB: Data from the Parsons et al. 2011 study: Background mutation...

BackRatesPancreas: Data from the Jones et al. 2008 study: Background mutation...

cma.fdr: Gene-level Empirical Bayes (EB) false discovery rate (FDR)...

cma.scores: Gene-level scores for the analysis of somatic point mutations...

cma.set.sim: Simulates data and performs gene-set analysis methods on the...

cma.set.stat: Implements gene-set analysis methods.

combine.sims: Combines two SetMethodSims objects.

EntrezID2Name: Map of gene IDs to gene names

extract.sims.method: Extracts the p-values or q-values from a SetMethodsSims...

GeneAlterBreast: Data from the Wood et al. 2007 and Sjoeblom et al. 2006...

GeneAlterColon: Data from the Wood et al. 2007 and Sjoeblom et al. 2006...

GeneAlterGBM: Data from the Parsons et al. 2008 study: Alterations for...

GeneAlterMB: Data from the Parsons et al. 2011 study: Alterations for...

GeneAlterPancreas: Data from the Jones et al. 2008 study: Alterations for every...

GeneCovBreast: Data from the Wood et al. 2007 and Sjoeblom et al. 2006...

GeneCovColon: Data from the Wood et al. 2007 and Sjoeblom et al. 2006...

GeneCovGBM: Data from the Parsons et al. 2008 study: Total number of...

GeneCovMB: Data from the Parsons et al. 2011 study: Total number of...

GeneCovPancreas: Data from the Jones et al. 2008 study: Total number of...

GeneID2Name11: Map of gene IDs to gene names for the Parsons et al. 2011...

GeneSampBreast: Data from the Wood et al. 2007 and Sjoeblom et al. 2006...

GeneSampColon: Data from the Wood et al. 2007 study: Number of samples for...

GeneSampGBM: Data from the Parsons et al. 2008 study: Number of samples...

GeneSampMB: Data from the Parsons et al. 2011 study: Number of samples...

GeneSampPancreas: Data from the Jones et al. 2008 study: Number of samples for...

SetMethodsSims-class: Class representation for depositing output from simulations.

Files in this package

CancerMutationAnalysis/DESCRIPTION
CancerMutationAnalysis/LICENSE
CancerMutationAnalysis/NAMESPACE
CancerMutationAnalysis/R
CancerMutationAnalysis/R/AllClasses.R CancerMutationAnalysis/R/add.zeroes.cma.data.R CancerMutationAnalysis/R/cma.fdr.R CancerMutationAnalysis/R/cma.scores.R CancerMutationAnalysis/R/cma.set.sim.R CancerMutationAnalysis/R/cma.set.stat.R CancerMutationAnalysis/R/cma.simulator.R CancerMutationAnalysis/R/ebfdr.R CancerMutationAnalysis/R/functions-for-SetMethods-Sims.R CancerMutationAnalysis/R/get.EventsBySampleBySet.from.EventsBySample.R CancerMutationAnalysis/R/get.cdf.het.berns.R CancerMutationAnalysis/R/get.p.vals.from.q.probs.R CancerMutationAnalysis/R/get.p.vals.from.q.probs.het.R CancerMutationAnalysis/R/get.p.vals.one.set.R CancerMutationAnalysis/R/get.stand.ts.R CancerMutationAnalysis/R/make.cov.obj.R CancerMutationAnalysis/R/make.mut.obj.R CancerMutationAnalysis/R/make.singled.out.samp.mut.R CancerMutationAnalysis/R/methods-SetMethodsSims.R CancerMutationAnalysis/R/p2q.R CancerMutationAnalysis/R/pass.null.het.p.values.R CancerMutationAnalysis/R/pass.null.p.values.R CancerMutationAnalysis/R/perm.null.het.p.values.R CancerMutationAnalysis/R/perm.null.p.values.R CancerMutationAnalysis/R/poisbin.R CancerMutationAnalysis/R/runGSEA.R CancerMutationAnalysis/R/shorten.gene.names.R CancerMutationAnalysis/R/sim.data.R CancerMutationAnalysis/R/sourceDir.R
CancerMutationAnalysis/README.md
CancerMutationAnalysis/build
CancerMutationAnalysis/build/vignette.rds
CancerMutationAnalysis/data
CancerMutationAnalysis/data/EntrezID2Name.RData
CancerMutationAnalysis/data/GeneID2Name11.RData
CancerMutationAnalysis/data/JonesPancreas08.RData
CancerMutationAnalysis/data/ParsonsGBM08.RData
CancerMutationAnalysis/data/ParsonsMB11.RData
CancerMutationAnalysis/data/WoodBreast07.RData
CancerMutationAnalysis/data/WoodColon07.RData
CancerMutationAnalysis/data/datalist
CancerMutationAnalysis/inst
CancerMutationAnalysis/inst/NEWS
CancerMutationAnalysis/inst/doc
CancerMutationAnalysis/inst/doc/CancerMutationAnalysis.R
CancerMutationAnalysis/inst/doc/CancerMutationAnalysis.Rnw
CancerMutationAnalysis/inst/doc/CancerMutationAnalysis.pdf
CancerMutationAnalysis/man
CancerMutationAnalysis/man/BackRatesBreast.Rd CancerMutationAnalysis/man/BackRatesColon.Rd CancerMutationAnalysis/man/BackRatesGBM.Rd CancerMutationAnalysis/man/BackRatesMB.Rd CancerMutationAnalysis/man/BackRatesPancreas.Rd CancerMutationAnalysis/man/EntrezID2Name.Rd CancerMutationAnalysis/man/GeneAlterBreast.Rd CancerMutationAnalysis/man/GeneAlterColon.Rd CancerMutationAnalysis/man/GeneAlterGBM.Rd CancerMutationAnalysis/man/GeneAlterMB.Rd CancerMutationAnalysis/man/GeneAlterPancreas.Rd CancerMutationAnalysis/man/GeneCovBreast.Rd CancerMutationAnalysis/man/GeneCovColon.Rd CancerMutationAnalysis/man/GeneCovGBM.Rd CancerMutationAnalysis/man/GeneCovMB.Rd CancerMutationAnalysis/man/GeneCovPancreas.Rd CancerMutationAnalysis/man/GeneID2Name11.Rd CancerMutationAnalysis/man/GeneSampBreast.Rd CancerMutationAnalysis/man/GeneSampColon.Rd CancerMutationAnalysis/man/GeneSampGBM.Rd CancerMutationAnalysis/man/GeneSampMB.Rd CancerMutationAnalysis/man/GeneSampPancreas.Rd CancerMutationAnalysis/man/SetMethodsSims-class.Rd CancerMutationAnalysis/man/cma.fdr.Rd CancerMutationAnalysis/man/cma.scores.Rd CancerMutationAnalysis/man/cma.set.sim.Rd CancerMutationAnalysis/man/cma.set.stat.Rd CancerMutationAnalysis/man/combine.sims.Rd CancerMutationAnalysis/man/extract.sims.method.Rd
CancerMutationAnalysis/src
CancerMutationAnalysis/src/get.cdf.het.berns.c
CancerMutationAnalysis/vignettes
CancerMutationAnalysis/vignettes/CancerMutationAnalysis.Rnw
CancerMutationAnalysis/vignettes/CancerMutationAnalysis.bib

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