Man pages for nvolkova/MutSim
Generating cancer mutations in genes according to mutational processes
| annotate_simulated_variants | Annotating base substitutions generated by... |
| cosine | Similarity function for signatures |
| gen_chrom | Chromosome generic |
| gen_chrom-GeneFeatures-method | Chromosome method for GeneFeatures class |
| gen_chrom-set | Assignable chromosome generic |
| gen_chrom-set-GeneFeatures-character-method | Chromosome replacement method for GeneFeatures class |
| GeneFeatures-class | An S4 class to represent a set of features of a gene. |
| generate_mutations | Generating base substitutions based on silent mutation rate |
| get_all_features | Get the required features for each gene |
| get_all_probabilities | Calculate mutation probability distribution per gene |
| get_chromosomes | Matching TxDb gene names with their chromosomes |
| min_ranges | Simplifying GRanges |
| MutSim | MutSim: A package for generating cancer mutations in genes... |
| name | Name generic |
| name-GeneFeatures-method | Name method for GeneFeatures class |
| name-set | Assignable name generic |
| name-set-GeneFeatures-character-method | Name replacement method for GeneFeatures class |
| positions | Positions generic |
| positions-GeneFeatures-method | Positions method for GeneFeatures class |
| positions-set | Assignable positions generic |
| positions-set-GeneFeatures-numeric-method | Positions replacement method for GeneFeatures class |
| RevCom | Simple reverse complement for trinuleotides |
| RevComMutType | Simple reverse complement for mutation types |
| tri.counts | tri.counts generic |
| tri.counts-GeneFeatures-method | tri.counts method for GeneFeatures class |
| tri.counts-set | Assignable tri.counts generic |
| tri.counts-set-GeneFeatures-numeric-method | tri.counts replacement method for GeneFeatures class |
| trinucleotides | Trinucleotides generic |
| trinucleotides-GeneFeatures-method | Trinucleotides method for GeneFeatures class |
| trinucleotides-set | Assignable trinucleotides generic |
| trinucleotides-set-GeneFeatures-character-method | Trinucleotides replacement method for GeneFeatures class |
| upload_signatures | Upload cancer signatures and mutation types from COSMIC |
