Cancer mutation analysis

[Up] [Top]

Documentation for package ‘CancerMutationAnalysis’ version 1.24.0

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.