Patient-oriented gene-set analysis

Documentation for package ‘PatientGeneSets’ version 1.0.0

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
EventsBySampleBrain	Data from Parsons et al. study: Mutation types for every gene and
extract.sims.method	Extracts the p-values or q-values from a SetMethodsSims object for a
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