cma.scores |
Cancer Mutation Prevalence Analysis Scores |
combine.sims |
Combines two SetMethodSims objects. |
Coverage |
Data from Parsons et al. study: Total number of nucleotides "at risk" |
CoverageBrain |
Data from Parsons et al. study: Total number of nucleotides "at risk" |
do.gene.set.analysis |
Implements gene-set analysis methods. |
EventsBySample |
Data from Parsons et al. study: Mutation types for every gene and sample |
EventsBySampleBrain |
Data from Parsons et al. study: Mutation types for every gene and sample |
extract.sims.method |
Extracts the p-values or q-values from a SetMethodsSims object for a specific method. |
GeneSizes |
Data from Parsons et al. study: Sizes and composition of RefSeq genes |
GeneSizes08 |
Data from Parsons et al. study: Sizes and composition of RefSeq genes |
ID2name |
Map of gene IDs to gene names |
Mutations |
Data from Parsons et al. study: Mutation counts |
MutationsBrain |
Data from Parsons et al. study: Mutation counts |
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. |
sim.data.p.values |
Simulates data and performs gene-set analysis methods on the simulated datasets. |