BackRatesBreast         Data from the Wood et al. 2007 study:
                        Background mutation rates
BackRatesColon          Data from the Wood et al. 2007 study:
                        Background mutation rates
BackRatesGBM            Data from the Parsons et al. 2008 study:
                        Background mutation rates
BackRatesMB             Data from the Parsons et al. 2011 study:
                        Background mutation rates
BackRatesPancreas       Data from the Jones et al. 2008 study:
                        Background mutation rates
EntrezID2Name           Map of gene IDs to gene names
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
GeneAlterGBM            Data from the Parsons et al. 2008 study:
                        Alterations for every gene and sample
GeneAlterMB             Data from the Parsons et al. 2011 study:
                        Alterations for every gene and sample
GeneAlterPancreas       Data from the Jones et al. 2008 study:
                        Alterations for every gene and sample
GeneCovBreast           Data from the Wood et al. 2007 and Sjoeblom et
                        al. 2006 studies: Total number of nucleotides
                        "at risk" ("coverage")
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")
GeneCovMB               Data from the Parsons et al. 2011 study: Total
                        number of nucleotides "at risk" ("coverage")
GeneCovPancreas         Data from the Jones et al. 2008 study: Total
                        number of nucleotides "at risk" ("coverage")
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
GeneSampColon           Data from the Wood et al. 2007 study: Number of
                        samples for each gene and screen type
GeneSampGBM             Data from the Parsons 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
GeneSampPancreas        Data from the Jones et al. 2008 study: Number
                        of samples for each gene and screen type
SetMethodsSims-class    Class representation for depositing output from
                        simulations.
cma.fdr                 Gene-level Empirical Bayes (EB) false discovery
                        rate (FDR) analysis for somatic mutations in
                        cancer
cma.scores              Gene-level scores for the analysis of somatic
                        point mutations in cancer
cma.set.sim             Simulates data and performs gene-set analysis
                        methods on the simulated datasets.
cma.set.stat            Implements gene-set analysis methods.
combine.sims            Combines two SetMethodSims objects.
extract.sims.method     Extracts the p-values or q-values from a
                        SetMethodsSims object for a specific method.
