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 |
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. |
EntrezID2Name |
Map of gene IDs to gene names |
extract.sims.method |
Extracts the p-values or q-values from a SetMethodsSims object for a specific method. |
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. |
SetMethodsSims-method |
Class representation for depositing output from simulations. |
show-method |
Class representation for depositing output from simulations. |