Patient-oriented gene-set analysis


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Documentation for package ‘PatientGeneSets’ version 1.4.0

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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.