| 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. |
