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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CancerMutationAnalysis")
AuthorGiovanni Parmigiani, Simina M. Boca
Bioconductor views Genetics Software
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.

Functions

BackRatesBreast Man page
BackRatesColon Man page
BackRatesGBM Man page
BackRatesMB Man page
BackRatesPancreas Man page
cma.fdr Man page
cma.scores Man page
cma.set.sim Man page
cma.set.stat Man page
combine.sims Man page
EntrezID2Name Man page
extract.sims.method 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
show,SetMethodsSims-method Man page

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.