# Patient-oriented gene-set analysis

## Documentation for package ‘PatientGeneSets’ version 1.4.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

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.