CancerMutationAnalysis: Cancer mutation analysis

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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.

Author
Giovanni Parmigiani, Simina M. Boca
Date of publication
None
Maintainer
Simina M. Boca <smb310@georgetown.edu>
License
GPL (>= 2) + file LICENSE
Version
1.16.0

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