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This is the release version of the CancerMutationAnalysis package on Bioconductor.

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Version

Version

1.14.0

License

GPL (>= 2) + file LICENSE

Maintainer

Simina M Boca

Last Published

February 15th, 2017

Functions in CancerMutationAnalysis (1.14.0)

cma.set.sim

Simulates data and performs gene-set analysis methods on the simulated datasets.
cma.scores

Gene-level scores for the analysis of somatic point mutations in cancer
GeneAlterMB

Data from the Parsons et al. 2011 study: Alterations for every gene and sample
GeneAlterGBM

Data from the Parsons et al. 2008 study: Alterations for every gene and sample
GeneSampPancreas

Data from the Jones et al. 2008 study: Number of samples for each gene and screen type
GeneSampMB

Data from the Parsons et al. 2011 study: Number of samples for each gene and screen type
BackRatesPancreas

Data from the Jones et al. 2008 study: Background mutation rates
cma.fdr

Gene-level Empirical Bayes (EB) false discovery rate (FDR) analysis for somatic mutations in cancer
GeneAlterBreast

Data from the Wood et al. 2007 and Sjoeblom et al. 2006 studies: Alterations for every gene and sample
GeneAlterColon

Data from the Wood et al. 2007 and Sjoeblom et al. 2006 studies: Alterations for every gene and sample
GeneCovPancreas

Data from the Jones et al. 2008 study: Total number of nucleotides "at risk" ("coverage")
GeneCovMB

Data from the Parsons et al. 2011 study: Total number of nucleotides "at risk" ("coverage")
BackRatesBreast

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

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

Data from the Parsons et al. 2008 study: Number of samples for each gene and screen type
GeneSampColon

Data from the Wood et al. 2007 study: Number of samples for each gene and screen type
GeneCovBreast

Data from the Wood et al. 2007 and Sjoeblom et al. 2006 studies: Total number of nucleotides "at risk" ("coverage")
GeneAlterPancreas

Data from the Jones et al. 2008 study: Alterations for every gene and sample
GeneCovColon

Data from the Wood et al. 2007 and Sjoeblom et al. 2006 studies: Total number of nucleotides "at risk" ("coverage")
GeneCovGBM

Data from the Parsons et al. 2008 study: Total number of nucleotides "at risk" ("coverage")
SetMethodsSims-class

Class representation for depositing output from simulations.
cma.set.stat

Implements gene-set analysis methods.
combine.sims

Combines two SetMethodSims objects.
GeneID2Name11

Map of gene IDs to gene names for the Parsons et al. 2011 medulloblastoma (MB) study
GeneSampBreast

Data from the Wood et al. 2007 and Sjoeblom et al. 2006 studies: Number of samples for each gene and screen type
BackRatesGBM

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

Data from the Parsons et al. 2011 study: Background mutation rates
extract.sims.method

Extracts the p-values or q-values from a SetMethodsSims object for a specific method.
EntrezID2Name

Map of gene IDs to gene names