# Comprehensive genome-wide analysis of mutational processes

## Documentation for package ‘MutationalPatterns’ version 3.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

MutationalPatterns-package | MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues
binomial_test | Binomial test for enrichment or depletion testing
bin_mutation_density | Bin the genome based on mutation density
calculate_lesion_segregation | Calculate the amount of lesion segregation for a GRangesList or GRanges object.
cluster_signatures | Signature clustering function
context_potential_damage_analysis | Potential damage analysis for the supplied mutational contexts
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 profiles/signatures
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 regions
explained_by_signatures | Defunct functions in package 'MutationalPattern'
extract_signatures | Extract mutational signatures from 96 mutation matrix using NMF
fit_to_signatures | Find optimal nonnegative linear combination of mutation signatures to reconstruct the mutation matrix.
fit_to_signatures_bootstrapped | Fit mutational signatures to a mutation matrix with bootstrapping
fit_to_signatures_strict | Fit mutational signatures to a mutation matrix with less overfitting
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.
get_sim_tb-method | 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
MutationalPatterns | MutationalPatterns: an integrative R package for studying patterns in base substitution catalogues
mutations_from_vcf | Retrieve base substitutions from vcf
mutation_context | Defunct functions in package 'MutationalPattern'
mutation_types | Defunct functions in package 'MutationalPattern'
mut_192_occurrences | Count 192 trinucleotide mutation occurrences
mut_96_occurrences | Count 96 trinucleotide mutation occurrences
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 information
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 contributions
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 reconstructed profile
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 pattern similarity analysis
rename_nmf_signatures | Rename NMF signatures based on previously defined signatures
show-method | An S4 method to show an instance of the region_cossim class.
signature_potential_damage_analysis | Potential damage analysis for the supplied mutational signatures
split_muts_region | Split GRangesList or GRanges based on a list of regions.
strand_bias_test | Significance test for strand asymmetry
strand_from_vcf | Defunct functions in package 'MutationalPattern'
strand_occurrences | Count occurrences per base substitution type and strand
type_context | Retrieve context of base substitution types