Man pages for CuppenResearch/MutationalPatterns
Comprehensive genome-wide analysis of mutational processes
| bin_mutation_density | Bin the genome based on mutation density |
| binomial_test | Binomial test for enrichment or depletion testing |
| calculate_lesion_segregation | Calculate the amount of lesion segregation for a GRangesList... |
| cluster_signatures | Signature clustering function |
| context_potential_damage_analysis | Potential damage analysis for the supplied mutational... |
| convert_sigs_to_ref | Convert tissue specific signature exposures to reference |
| cos_sim | Cosine similarity function |
| cos_sim_matrix | Compute all pairwise cosine similarities between mutational... |
| count_dbs_contexts | Count DBS contexts |
| count_indel_contexts | Count indel contexts |
| count_mbs_contexts | Count MBS variants grouped by length. |
| determine_regional_similarity | Determine regional mutation pattern similarity |
| enrichment_depletion_test | Test for enrichment or depletion of mutations in genomic... |
| extract_signatures | Extract mutational signatures from 96 mutation matrix using... |
| fit_to_signatures | Find optimal nonnegative linear combination of mutation... |
| fit_to_signatures_bootstrapped | Fit mutational signatures to a mutation matrix with... |
| fit_to_signatures_strict | Fit mutational signatures to a mutation matrix with less... |
| genomic_distribution | Find overlaps between mutations and a genomic region. |
| get_dbs_context | Get DBS context |
| get_indel_context | Get indel contexts |
| get_known_signatures | Get known signatures |
| get_mut_type | Get variants with mut_type from GRanges |
| get_sim_tb | An S4 generic to get the sim_tb from a region_cossim object. |
| lengthen_mut_matrix | Lengthen mutation matrix |
| merge_signatures | Merge signatures based on cosine similarity |
| mut_192_occurrences | Count 192 trinucleotide mutation occurrences |
| mut_96_occurrences | Count 96 trinucleotide mutation occurrences |
| MutationalPatterns-defunct | Defunct functions in package 'MutationalPattern' |
| MutationalPatterns-package | MutationalPatterns: an integrative R package for studying... |
| mutations_from_vcf | Retrieve base substitutions from vcf |
| mut_context | Retrieve context of base substitutions |
| mut_matrix | Make mutation count matrix of 96 trinucleotides |
| mut_matrix_stranded | Make mutation count matrix of 96 trinucleotides with strand... |
| mut_strand | Find strand of mutations |
| mut_type | Retrieve base substitution types from a VCF object |
| mut_type_occurrences | Count the occurrences of each base substitution type |
| plot_192_profile | Plot 192 trinucleotide profile |
| plot_96_profile | Plot 96 trinucleotide profile |
| plot_bootstrapped_contribution | Plot the bootstrapped signature contributions |
| plot_compare_dbs | Compare two DBS mutation profiles |
| plot_compare_indels | Compare two indel mutation profiles |
| plot_compare_mbs | Compare two mbs mutation profiles |
| plot_compare_profiles | Compare two 96 mutation profiles |
| plot_contribution | Plot signature contribution barplot |
| plot_contribution_heatmap | Plot signature contribution heatmap |
| plot_correlation_bootstrap | Plots the correlation between bootstrapped signature... |
| plot_cosine_heatmap | Plot cosine similarity heatmap |
| plot_dbs_contexts | Plot the DBS contexts |
| plot_enrichment_depletion | Plot enrichment/depletion of mutations in genomic regions |
| plot_indel_contexts | Plot the indel contexts |
| plot_lesion_segregation | Plot the strands of variants to show lesion segregation |
| plot_main_dbs_contexts | Plot the main DBS contexts |
| plot_main_indel_contexts | Plot the main indel contexts |
| plot_mbs_contexts | Plot the MBS contexts |
| plot_original_vs_reconstructed | Plot the similarity between a mutation matrix and its... |
| plot_profile_heatmap | Plot a mutation matrix as a heatmap |
| plot_profile_region | Plot 96 trinucleotide profile per subgroup |
| plot_rainfall | Plot genomic rainfall |
| plot_regional_similarity | Plot regional similarity |
| plot_river | Plot a riverplot |
| plot_signature_strand_bias | Plot signature strand bias |
| plot_spectrum | Plot point mutation spectrum |
| plot_spectrum_region | Plot point mutation spectrum per genomic region |
| plot_strand | Plot strand per base substitution type |
| plot_strand_bias | Plot strand bias per base substitution type per group |
| pool_mut_mat | Pool multiple samples from a mutation matrix together |
| read_vcfs_as_granges | Read VCF files into a GRangesList |
| region_cossim-class | An S4 class to store the results of a regional mutation... |
| rename_nmf_signatures | Rename NMF signatures based on previously defined signatures |
| show-region_cossim-method | An S4 method to show an instance of the region_cossim class. |
| signature_potential_damage_analysis | Potential damage analysis for the supplied mutational... |
| split_muts_region | Split GRangesList or GRanges based on a list of regions. |
| strand_bias_test | Significance test for strand asymmetry |
| strand_occurrences | Count occurrences per base substitution type and strand |
| type_context | Retrieve context of base substitution types |
