# Cancer mutation analysis

## Documentation for package ‘CancerMutationAnalysis’ version 1.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.