CancerMutationAnalysis: Cancer mutation analysis
Version 1.18.0

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
Bioconductor views Genetics Software
Date of publicationNone
MaintainerSimina M. Boca <smb310@georgetown.edu>
LicenseGPL (>= 2) + file LICENSE
Version1.18.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CancerMutationAnalysis")

Getting started

README.md

Popular man pages

BackRatesMB: Data from the Parsons et al. 2011 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.stat: Implements gene-set analysis methods.
GeneAlterMB: Data from the Parsons et al. 2011 study: Alterations for...
GeneCovBreast: Data from the Wood et al. 2007 and Sjoeblom et al. 2006...
GeneSampPancreas: Data from the Jones et al. 2008 study: Number of samples for...
See all...

All man pages Function index File listing

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.

Functions

BackRatesBreast Man page
BackRatesColon Man page
BackRatesGBM Man page
BackRatesMB Man page
BackRatesPancreas Man page
EntrezID2Name Man page
GeneAlterBreast Man page
GeneAlterColon Man page
GeneAlterGBM Man page
GeneAlterMB Man page
GeneAlterPancreas Man page
GeneCovBreast Man page
GeneCovColon Man page
GeneCovGBM Man page
GeneCovMB Man page
GeneCovPancreas Man page
GeneID2Name11 Man page
GeneSampBreast Man page
GeneSampColon Man page
GeneSampGBM Man page
GeneSampMB Man page
GeneSampPancreas Man page
SetMethodsSims-class Man page
SetMethodsSims-method Man page
add.zeroes.cma.data Source code
cma.fdr Man page Source code
cma.scores Man page Source code
cma.set.sim Man page Source code
cma.set.stat Man page Source code
cma.simulator Source code
combine.sims Man page Source code
ebfdr Source code
extract.sims.method Man page Source code
get.EventsBySampleBySet.from.EventsBySample Source code
get.cdf.het.berns Source code
get.p.vals.from.q.probs Source code
get.p.vals.from.q.probs.het Source code
get.p.vals.one.set Source code
get.stand.ts Source code
make.cov.obj Source code
make.mut.obj Source code
make.singled.out.samp.mut Source code
p2q Source code
pass.null.het.p.values Source code
pass.null.p.values Source code
perm.null.het.p.values Source code
perm.null.p.values Source code
poisbin Source code
runGSEA Source code
shorten.gene.names Source code
show,SetMethodsSims-method Man page
sim.data Source code
sourceDir Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
R
R/AllClasses.R
R/add.zeroes.cma.data.R
R/cma.fdr.R
R/cma.scores.R
R/cma.set.sim.R
R/cma.set.stat.R
R/cma.simulator.R
R/ebfdr.R
R/functions-for-SetMethods-Sims.R
R/get.EventsBySampleBySet.from.EventsBySample.R
R/get.cdf.het.berns.R
R/get.p.vals.from.q.probs.R
R/get.p.vals.from.q.probs.het.R
R/get.p.vals.one.set.R
R/get.stand.ts.R
R/make.cov.obj.R
R/make.mut.obj.R
R/make.singled.out.samp.mut.R
R/methods-SetMethodsSims.R
R/p2q.R
R/pass.null.het.p.values.R
R/pass.null.p.values.R
R/perm.null.het.p.values.R
R/perm.null.p.values.R
R/poisbin.R
R/runGSEA.R
R/shorten.gene.names.R
R/sim.data.R
R/sourceDir.R
README.md
build
build/vignette.rds
data
data/EntrezID2Name.RData
data/GeneID2Name11.RData
data/JonesPancreas08.RData
data/ParsonsGBM08.RData
data/ParsonsMB11.RData
data/WoodBreast07.RData
data/WoodColon07.RData
data/datalist
inst
inst/NEWS
inst/doc
inst/doc/CancerMutationAnalysis.R
inst/doc/CancerMutationAnalysis.Rnw
inst/doc/CancerMutationAnalysis.pdf
man
man/BackRatesBreast.Rd
man/BackRatesColon.Rd
man/BackRatesGBM.Rd
man/BackRatesMB.Rd
man/BackRatesPancreas.Rd
man/EntrezID2Name.Rd
man/GeneAlterBreast.Rd
man/GeneAlterColon.Rd
man/GeneAlterGBM.Rd
man/GeneAlterMB.Rd
man/GeneAlterPancreas.Rd
man/GeneCovBreast.Rd
man/GeneCovColon.Rd
man/GeneCovGBM.Rd
man/GeneCovMB.Rd
man/GeneCovPancreas.Rd
man/GeneID2Name11.Rd
man/GeneSampBreast.Rd
man/GeneSampColon.Rd
man/GeneSampGBM.Rd
man/GeneSampMB.Rd
man/GeneSampPancreas.Rd
man/SetMethodsSims-class.Rd
man/cma.fdr.Rd
man/cma.scores.Rd
man/cma.set.sim.Rd
man/cma.set.stat.Rd
man/combine.sims.Rd
man/extract.sims.method.Rd
src
src/get.cdf.het.berns.c
vignettes
vignettes/CancerMutationAnalysis.Rnw
vignettes/CancerMutationAnalysis.bib
CancerMutationAnalysis documentation built on May 20, 2017, 9:59 p.m.

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